Genome assembly PDT002037147.1

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Submitted GenBank assembly
GCA_034572275.1
Taxon
Salmonella enterica subsp. enterica serovar Kentucky
Strain
SAL-22-VL-WA-MO-0034
WGS project
ABPPGC01
Submitter
Vet-LIRN-CVM-FDA
Date
Dec 25, 2023

Genome notes

NCBI has noted the following for this genome assembly. View definitions

  • from large multi-isolate project

Assembly statistics

GenBank
Genome size5.2 Mb
Total ungapped length5.2 Mb
Number of contigs68
Contig N50293.6 kb
Contig L507
GC percent52
Genome coverage98.0x
Assembly levelContig

Sample details

BioSample ID
SAMN38982114
Description
One Health Enteric sample from Salmonella enterica subsp. enterica serovar Kentucky
Submitter
Vet-LIRN: Washington State University, Animal Disease Diagnostic Laboratory
Strain
SAL-22-VL-WA-MO-0034
Collected by
University of Missouri Veterinary Medical Diagnostic Laboratory
Collection date
2022-12
Geographic location
USA:IL
Isolation source
intestine
Source type
animal
Purpose of sampling
not collected
Project name
Vet-LIRN-SAL-WA
Serovar
Kentucky
Sequenced by
Washington State University Washington Animal Disease Diagnostic Laboratory
Host
Gallus gallus domesticus
Host disease
Enteritis
Sub species
enterica
Sample name
SAL-22-VL-WA-MO-0034
SRA
SRS19955710
Models
One Health Enteric
Package
OneHealthEnteric.1.0
Submission date
2023-12-20T15:33:08.173
Publication date
2023-12-21T00:00:00.000
Last updated
2023-12-21T12:34:21.980

Assembly methods

Sequencing technology
ILLUMINA
Comment

The annotation was added by the assembly submitters using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about stand-alone PGAP can be found here: https://github.com/ncbi/pgap/

This draft WGS assembly was generated by running SKESA to generate a de-novo assembly. The de-novo assembly was then concatenated with contigs generated using a guided assembler using antimicrobial resistance genes as baits to comprehensively catalog the set of resistance genes in the isolate. Note, some parts of the contigs derived from the guided assembler may overlap de-novo contigs, and other guided assembler contigs. De-novo contigs can be differentiated from guided assembler contigs by their names , which include either 'denovo' or 'guided'.

Assembly method
SKESA v. 2.2

Additional genomes

Browse all Salmonella enterica genomes (581968)

BioProject

PRJNA481328

Vet-LIRN-SAL-WA (Vet-LIRN-CVM-FDA)

Pathogen Detection Resource

Annotation details

GenBank
ProviderNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateDec 23, 2023
Genes5,046
Protein-coding4,804
Software version2021-01-11.build5132

About PGAP

The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) uses multiple approaches to predict protein-coding and RNA genes and other functional elements directly from sequence.

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Quality analysis

Taxonomy check

Taxonomy check status
OK
Best match status
derived_species_match
Submitted organism name
Salmonella enterica subsp. enterica serovar Kentucky
Submitted species name
Salmonella enterica

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_014334155.1GCA_014334155.1
Organism nameSalmonella enterica subsp. enterica serovar TyphimuriumSalmonella enterica
Type categorytypetype
ANI98.73%98.73%
Assembly coverage84.61%84.61%
Type assembly coverage90.56%90.56%

Chromosomes

Note: This contig-level genome assembly includes 68 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_034572275.1

n/a

PDT002037147.1ContigDec 25, 2023