Genome assembly PDT001924375.1

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Submitted GenBank assembly
GCA_032621335.1
Taxon
Salmonella enterica subsp. enterica serovar Rubislaw
Strain
SAL-23-VL-SD-NC-0002
WGS project
ABNSKD01
Submitter
Vet-LIRN-CVM-FDA
Date
Oct 13, 2023

Genome notes

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

  • from large multi-isolate project

Assembly statistics

GenBank
Genome size4.8 Mb
Total ungapped length4.8 Mb
Number of contigs49
Contig N50307.4 kb
Contig L506
GC percent52
Genome coverage117.0x
Assembly levelContig

Sample details

BioSample ID
SAMN37706711
Description
One Health Enteric sample from Salmonella enterica subsp. enterica serovar Rubislaw
Submitter
Vet-LIRN Project: SDSU Veterinary & Biomedical Sciences/ DOH South Dakota
Strain
SAL-23-VL-SD-NC-0002
Collected by
North Carolina State University|College of Veterinary Medicine
Collection date
Jan 13, 2023
Geographic location
USA:NC
Isolation source
feces
Source type
animal
Purpose of sampling
case investigation
Project name
Vet-LIRN
Sequenced by
South Dakota State University|South Dakota Animal Disease Research and Diagnostic Laboratory
Host
Equus caballus
Host disease
colitis
Serovar
Rubislaw
Sub species
enterica
Latitude and longitude
not collected
Sample name
SAL-23-VL-SD-NC-0002
SRA
SRS19125893
Models
One Health Enteric
Package
OneHealthEnteric.1.0
Submission date
2023-10-06T12:20:08.083
Publication date
2023-10-06T00:00:00.000
Last updated
2024-12-20T11:10:14.323

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

Annotation details

GenBank
ProviderNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateOct 12, 2023
Genes4,644
Protein-coding4,460
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.

Continue reading

Quality analysis

Taxonomy check

Taxonomy check status
OK
Best match status
derived_species_match
Submitted organism name
Salmonella enterica subsp. enterica serovar Rubislaw
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
ANI98.5%98.5%
Assembly coverage90.21%90.21%
Type assembly coverage87.59%87.59%

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_032621335.1

n/a

PDT001924375.1ContigOct 13, 2023