Genome assembly PDT000257495.2

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Submitted GenBank assembly
GCA_009565995.1
Taxon
Salmonella enterica subsp. enterica serovar Typhimurium
Isolate
AUSMDU00003846
WGS project
AAMYMK01
Submitter
Microbiological Diagnostics Unit
Date
Nov 5, 2019

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 contigs197
Contig N5050.3 kb
Contig L5032
GC percent52
Genome coverage129.0x
Assembly levelContig

Sample details

BioSample ID
SAMN05162830
Description
Pathogen: clinical or host-associated sample from Salmonella enterica subsp. enterica serovar Typhimurium
Submitter
Microbiological Diagnostics Unit
Isolate
AUSMDU00003846
Collected by
not collected
Collection date
2014
Geographic location
Australia
Host
Homo sapiens
Isolation source
human
Latitude and longitude
not collected
Serovar
Typhimurium
Sub species
enterica
Sample name
AUSMDU00003846
SRA
SRS1461854
Models
Pathogen.cl
Package
Pathogen.cl.1.0
Submission date
2016-05-23T05:44:18.000
Publication date
2017-06-23T00:00:00.000
Last updated
2019-05-23T15:50:38.464

Assembly methods

Sequencing technology
ILLUMINA
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/

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

BioProject

PRJNA322428

Genomics links sporadic salmonellosis to outbreaks

Annotation details

GenBank
ProviderNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateNov 3, 2019
Genes4,937
Protein-coding4,744
Software version4.9

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
ANI99.94%99.94%
Assembly coverage96.75%96.75%
Type assembly coverage97.18%97.18%

Chromosomes

Note: This contig-level genome assembly includes 197 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_009565995.1

n/a

PDT000257495.2ContigNov 5, 2019