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ASM2426640v1

Organism name:
Salmonella enterica subsp. enterica serovar Thompson (enterobacteria)
Taxonomy check:
OK
Infraspecific name:
Serovar: Thompson
Infraspecific name:
Strain: R18.0872
BioSample:
SAMN29431226
BioProject:
PRJNA478278
Submitter:
Centers for Disease Control, Taiwan
Date:
2022/07/14
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
GenBank assembly accession:
GCA_024266405.1 (latest)
RefSeq assembly accession:
GCF_024266405.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
flye v. 2.9; trycycler v. 0.5.3; medaka v. 1.6.0; homopolish v. 0.3.3; polca v. 4.0.5; polypolish v. 0.5.0
Expected final version:
no
Genome coverage:
324x
Sequencing technology:
Illumina MiSeq; Oxford Nanopore MinION

IDs: 13278531 [UID] 34686108 [GenBank] 34697468 [RefSeq]

See Genome Information for Salmonella enterica

Pathogen Detection Resources

There are 533578 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/

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Date::07/23/2023 02:11:33
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)::4,990
CDSs (total)::4,868
Genes (coding)::4,740
CDSs (with protein)::4,740
Genes (RNA)::122
rRNAs::8, 7, 7 (5S, 16S, 23S)
complete rRNAs::8, 7, 7 (5S, 16S, 23S)
tRNAs::88
ncRNAs::12
Pseudo Genes (total)::128
CDSs (without protein)::128
Pseudo Genes (ambiguous residues)::0 of 128
Pseudo Genes (frameshifted)::50 of 128
Pseudo Genes (incomplete)::95 of 128
Pseudo Genes (internal stop)::26 of 128
Pseudo Genes (multiple problems)::40 of 128
Pseudo Genes (short protein)::1 of 128
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,057,910
Total ungapped length5,057,910
Total number of chromosomes and plasmids5

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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_024266415.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP100702.1=NZ_CP100702.1
Plasmid pR18.0872_149kCP100703.1=NZ_CP100703.1
Plasmid pR18.0872_16kCP100706.1=NZ_CP100706.1
Plasmid pR18.0872_35kCP100705.1=NZ_CP100705.1
Plasmid pR18.0872_93kCP100704.1=NZ_CP100704.1

Assembly statistics

MoleculeTotal
Length
All5,057,910
Chromosome 4,764,385
Plasmid pR18.0872_149k149,266
Plasmid pR18.0872_16k15,860
Plasmid pR18.0872_35k35,226
Plasmid pR18.0872_93k93,173

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Salmonella enterica subsp. enterica serovar ThompsonSalmonella enterica

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_016028495.1Salmonella entericatype

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_016028495.1Salmonella entericatype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type98.9989.2590.85
Best-match type98.9989.2590.85

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna