Genome assembly PDT000863462.1

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Submitted GenBank assembly
GCA_014949865.1
Taxon
Salmonella enterica subsp. enterica serovar Typhimurium
Strain
SAL-20-VL-WA-KY-0004
WGS project
AAWOJD01
Submitter
Vet-LIRN-CVM-FDA
Date
Oct 26, 2020

Genome notes

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

  • from large multi-isolate project

Assembly statistics

GenBank
Genome size5 Mb
Total ungapped length5 Mb
Number of contigs49
Contig N50210.2 kb
Contig L508
GC percent52
Genome coverage126.0x
Assembly levelContig

Sample details

BioSample ID
SAMN16480836
Description
Pathogen: environmental/food/other sample from Salmonella enterica subsp. enterica serovar Typhimurium
Submitter
FDA Center for Food Safety and Applied Nutrition
Isolation source
Colon
Interagency Food Safety Analytics Collaboration (IFSAC) category
veterinary clinical/research| other animal
Source type
animal
Strain
SAL-20-VL-WA-KY-0004
Collection date
Apr 17, 2020
PublicAccession
CFSAN106945
Attribute package
environmental/food/other
Genus
Salmonella
Geographic location
USA:KY
Isolate name alias
CFSAN106945
Collected by
University of Kentucky Veterinary Diagnostic Laboratory
Species
enterica
ProjectAccession
PRJNA481328
Ontological term
colon:UBERON_0001155, equus caballus:NCBITAXON_9796
Sub species
enterica
Serovar
Typhimurium
Host
Equus caballus
Project name
Vet-LIRN-SAL-WA
Sequenced by
Washington State University Washington Animal Disease Diagnostic Laboratory
SRA
SRS7537575
CFSAN
CFSAN106945
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2020-10-19T21:16:10.620
Publication date
2020-10-19T00:00:00.000
Last updated
2024-12-20T11:44:18.526

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)
DateOct 20, 2020
Genes4,902
Protein-coding4,736
Software version2020-02-06.build4373

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.

Continue reading

Quality analysis

Taxonomy check

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

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_000006945.2GCA_000006945.2
Organism nameSalmonella enterica subsp. enterica serovar Typhimurium str. LT2Salmonella enterica
Type categorytypetype
ANI99.97%99.97%
Assembly coverage93.77%93.77%
Type assembly coverage95.43%95.43%

Chromosomes

Note: This contig-level genome assembly includes 49 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_014949865.1

n/a

PDT000863462.1ContigOct 26, 2020