Genome assembly ASM171662v1

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NCBI RefSeq assembly
GCF_001716625.1
Submitted GenBank assembly
GCA_001716625.1
Taxon
Salmonella enterica subsp. enterica serovar Kentucky
Strain
ARS-CC8446
WGS project
MCPW01
Submitter
USDA
Date
Aug 29, 2016

Assembly statistics

RefSeqGenBank
Genome size4.8 Mb4.8 Mb
Total ungapped length4.8 Mb4.8 Mb
Number of contigs6565
Contig N50527.1 kb527.1 kb
Contig L5044
GC percent5252
Genome coverage40.0x40.0x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN05390909
Description
Pathogen: environmental/food/other sample from Salmonella enterica subsp. enterica serovar Kentucky
Submitter
USDA
Strain
ARS-CC8446
Latitude and longitude
not collected
Collection date
2014
Geographic location
USA:OH
Isolation source
Milk filter (dairy cow farm)
Serovar
Kentucky
Collected by
USDA-ARS
Sample number
29
Host
Bos taurus
Sub species
enterica
Sample name
ARS-CC8446
SRA
SRS1608034
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2016-07-14T11:53:04.960
Publication date
2016-08-12T00:00:00.000
Last updated
2022-02-28T19:53:20.472

Assembly methods

Sequencing technology
Illumina NextSeq 500
Comment
Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
Assembly method
SPAdes v. 3.6.2

Additional genomes

Browse all Salmonella enterica genomes (582812)

BioProject

PRJNA337914

Salmonella enterica Genome sequencing and assembly

Pathogen Detection Resource

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_001716625.1-RS_2024_12_28NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateDec 28, 2024Aug 8, 2016
Genes4,7114,654
Protein-coding4,4774,477
Software version6.93.3

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

CheckM analysis (v1.2.3)

Completeness: 99.64% (68th Percentile)

Contamination: 0.98%

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
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_001558355.2GCA_001558355.2
Organism nameSalmonella entericaSalmonella enterica
Type categorytypetype
ANI98.73%98.73%
Assembly coverage90.97%90.97%
Type assembly coverage88.89%88.89%

Chromosomes

Note: This contig-level genome assembly includes 65 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_001716625.1GCF_001716625.1ASM171662v1ContigAug 29, 2016