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Organism name:
Yersinia pestis Nepal516 (enterobacteria)
Taxonomy check:
Infraspecific name:
Strain: Nepal516
DOE Joint Genome Institute
Assembly type:
Assembly level:
Complete Genome
Genome representation:
GenBank assembly accession:
GCA_000013805.1 (latest)
RefSeq assembly accession:
GCF_000013805.1 (latest)
RefSeq assembly and GenBank assembly identical:

IDs: 34908 [UID] 14608 [GenBank] 34908 [RefSeq]

See Genome Information for Yersinia pestis

There are 685 assemblies for this organism

See more

History (Show revision history)


URL -- http://www.jgi.doe.gov
JGI Project ID: 2773192
Source DNA and bacteria available from Gary Andersen (glandersen@lbl.gov)
Contacts: Gary Andersen (glandersen@lbl.gov)
 Paul Richardson (microbes@cuba.jgi-psf.org)
Annotation done by JGI-ORNL
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


Annotation Provider::NCBI RefSeq
Annotation Date::02/13/2022 01:41:48
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::6.0
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::4,204
CDSs (total)::4,100
Genes (coding)::3,913
CDSs (with protein)::3,913
Genes (RNA)::104
rRNAs::8, 7, 7 (5S, 16S, 23S)
complete rRNAs::8, 7, 7 (5S, 16S, 23S)
Pseudo Genes (total)::187
CDSs (without protein)::187
Pseudo Genes (ambiguous residues)::0 of 187
Pseudo Genes (frameshifted)::83 of 187
Pseudo Genes (incomplete)::118 of 187
Pseudo Genes (internal stop)::27 of 187
Pseudo Genes (multiple problems)::31 of 187
CRISPR Arrays::1

Global statistics

Total sequence length4,646,286
Total ungapped length4,646,286
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_000013815.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP000305.1=NC_008149.1
Plasmid pMTCP000306.1=NC_008118.1
Plasmid pPCPCP000307.1=NC_008119.1

Assembly statistics

Chromosome 4,534,590
Plasmid pMT100,918
Plasmid pPCP10,778

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Yersinia pestis Nepal516Yersinia pestis

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_900460465.1Yersinia pestissuspected-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_900460465.1Yersinia pestissuspected-type

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type99.9598.6295.92
Best-match type99.9598.6295.92

ANI result

Taxonomy check statusBest match statusComment
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