Genome assembly PDT000863462.1
- 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 size | 5 Mb |
Total ungapped length | 5 Mb |
Number of contigs | 49 |
Contig N50 | 210.2 kb |
Contig L50 | 8 |
GC percent | 52 |
Genome coverage | 126.0x |
Assembly level | Contig |
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
PRJNA481328Vet-LIRN-SAL-WA (Vet-LIRN-CVM-FDA)
Pathogen Detection Resource
Annotation details
GenBank | |
---|---|
Provider | NCBI |
Name | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Oct 20, 2020 |
Genes | 4,902 |
Protein-coding | 4,736 |
Software version | 2020-02-06.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 readingQuality 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 organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_000006945.2 | GCA_000006945.2 |
Organism name | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | Salmonella enterica |
Type category | type | type |
ANI | 99.97% | 99.97% |
Assembly coverage | 93.77% | 93.77% |
Type assembly coverage | 95.43% | 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 | PDT000863462.1 | Contig | Oct 26, 2020 |