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EcRM9872

Organism name:
Escherichia coli O145 str. RM9872 (E. coli)
Taxonomy check:
OK
Infraspecific name:
Strain: RM9872
BioSample:
SAMN08724661
BioProject:
PRJNA69939
Submitter:
USDA-ARS-WRRC-PSM
Date:
2018/05/30
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
GenBank assembly accession:
GCA_003586065.1 (latest)
RefSeq assembly accession:
GCF_003586065.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
HGAP v.3 as available in the SMRT Analysis v. 2.3; Geneious Reference Assembly v. 11.1
Expected final version:
yes
Genome coverage:
287.0x
Sequencing technology:
PacBio; Illumina MiSeq

IDs: 1987691 [UID] 7476648 [GenBank] 7490428 [RefSeq]

See Genome Information for Escherichia coli

Pathogen Detection Resources

There are 270130 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/
Bacteria and source DNA available from Craig Parker, USDA ARS PSMRU, 800 Buchanan St. Albany, CA 94710.

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Date::06/01/2023 18:47:04
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::6.5
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA
Genes (total)::5,403
CDSs (total)::5,270
Genes (coding)::4,980
CDSs (with protein)::4,980
Genes (RNA)::133
rRNAs::8, 7, 7 (5S, 16S, 23S)
complete rRNAs::8, 7, 7 (5S, 16S, 23S)
tRNAs::103
ncRNAs::8
Pseudo Genes (total)::290
CDSs (without protein)::290
Pseudo Genes (ambiguous residues)::0 of 290
Pseudo Genes (frameshifted)::113 of 290
Pseudo Genes (incomplete)::178 of 290
Pseudo Genes (internal stop)::59 of 290
Pseudo Genes (multiple problems)::53 of 290
Pseudo Genes (short protein)::3 of 290
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,475,442
Total ungapped length5,475,442
Total number of chromosomes and plasmids2

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Assembly Information

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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_003586075.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP028379.1=NZ_CP028379.1
Plasmid pRM9872-1CP028380.1=NZ_CP028380.1

Assembly statistics

MoleculeTotal
Length
All5,475,442
Chromosome 5,385,924
Plasmid pRM9872-189,518

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Escherichia coli O145 str. RM9872Escherichia coli

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_001281725.1Escherichia colicladeref

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_001281725.1Escherichia colicladeref

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type98.4385.9988.84
Best-match type98.4385.9988.84

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna