Genome assembly ASM205874v1

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NCBI RefSeq assembly
GCF_002058745.1
Submitted GenBank assembly
GCA_002058745.1
Taxon
Salmonella enterica subsp. enterica serovar Litchfield
Strain
BCW_4015
WGS project
MYTV01
Submitter
University of California at Davis
Date
Mar 21, 2017

Assembly statistics

RefSeqGenBank
Genome size4.8 Mb4.8 Mb
Total ungapped length4.8 Mb4.8 Mb
Number of contigs172172
Contig N5067.8 kb67.8 kb
Contig L502323
GC percent5252
Genome coverage62.0x62.0x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN02368825
Description
Pathogen sample from Salmonella enterica
Submitter
University of California at Davis 100K Pathogen Genome Project
Collected by
CDC
Sub species
enterica
Host
Homo sapiens
Serovar
Litchfield
Strain
BCW_4015
Collection date
2012
Geographic location
USA:MI
Isolate name alias
CDC_2012K-1782
Sample name
BCW_4015
SRA
SRS528886
Models
Pathogen, clinical/host-associated
Package
Pathogen.cl.1.0
Submission date
2013-09-27T20:43:12.276
Publication date
2014-10-05T00:00:00.000
Last updated
2021-02-10T11:17:05.256

Assembly methods

Sequencing technology
Illumina HiSeq
Comment
Bacteria available from Dr. Bart C. Weimer.
Assembly method
SPAdes v. 3.9.0

Additional genomes

Browse all Salmonella enterica genomes (581968)

BioProject

PRJNA203445

Major food bacterial pathogens in the united states and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, and Vibrio parahaemolyticus genome sequencing

Pathogen Detection Resource

Annotation details

RefSeq
ProviderNCBI RefSeq
NameGCF_002058745.1-RS_2024_05_13
DateMay 13, 2024
Genes4,730
Protein-coding4,492
Software version6.7

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

CheckM analysis (v1.2.2)

Completeness: 99.67% (73rd Percentile)

Contamination: 1.13%

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Salmonella enterica CheckM marker set. For more information on CheckM, see Parks, et al. Genome Res (2015).

Taxonomy check

Taxonomy check status
OK
Best match status
derived_species_match
Submitted organism name
Salmonella enterica subsp. enterica serovar Litchfield
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
ANI99.01%99.01%
Assembly coverage93.49%93.49%
Type assembly coverage90.2%90.2%

Chromosomes

Note: This contig-level genome assembly includes 172 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_002058745.1GCF_002058745.1ASM205874v1ContigMar 21, 2017