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ASM966404v1

Organism name:
Citrobacter freundii (enterobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: 565
BioSample:
SAMN11288321
BioProject:
PRJNA529867
Submitter:
IHU mediterranee infection
Date:
2019/11/15
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
GenBank assembly accession:
GCA_009664045.1 (latest)
RefSeq assembly accession:
GCF_009664045.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
SPAdes v. 3.12.0
Expected final version:
yes
Genome coverage:
32.0x
Sequencing technology:
Illumina MiSeq; Oxford Nanopore MiniION

IDs: 5323981 [UID] 15412458 [GenBank] 15416568 [RefSeq]

See Genome Information for Citrobacter freundii

There are 2639 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/

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Date::01/24/2024 13:44:20
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)::5,397
CDSs (total)::5,275
Genes (coding)::5,159
CDSs (with protein)::5,159
Genes (RNA)::122
rRNAs::9, 8, 8 (5S, 16S, 23S)
complete rRNAs::9, 8, 8 (5S, 16S, 23S)
tRNAs::87
ncRNAs::10
Pseudo Genes (total)::116
CDSs (without protein)::116
Pseudo Genes (ambiguous residues)::0 of 116
Pseudo Genes (frameshifted)::32 of 116
Pseudo Genes (incomplete)::72 of 116
Pseudo Genes (internal stop)::24 of 116
Pseudo Genes (multiple problems)::13 of 116
Pseudo Genes (short protein)::1 of 116
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,471,065
Total ungapped length5,471,065
Total number of chromosomes and plasmids2

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_009664055.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP038656.1=NZ_CP038656.1
Plasmid p565_1CP038657.1=NZ_CP038657.1

Assembly statistics

MoleculeTotal
Length
All5,471,065
Chromosome 5,207,876
Plasmid p565_1263,189

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Citrobacter freundiiCitrobacter freundii

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_900635425.1Citrobacter freundiitype

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_900635425.1Citrobacter freundiitype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type98.5679.8488.06
Best-match type98.5679.8488.06

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna