Genome assembly ASM205874v1
- 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
RefSeq | GenBank | |
---|---|---|
Genome size | 4.8 Mb | 4.8 Mb |
Total ungapped length | 4.8 Mb | 4.8 Mb |
Number of contigs | 172 | 172 |
Contig N50 | 67.8 kb | 67.8 kb |
Contig L50 | 23 | 23 |
GC percent | 52 | 52 |
Genome coverage | 62.0x | 62.0x |
Assembly level | Contig | Contig |
View sequences | view RefSeq sequences | view 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
PRJNA203445Major 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 | |
---|---|
Provider | NCBI RefSeq |
Name | GCF_002058745.1-RS_2024_05_13 |
Date | May 13, 2024 |
Genes | 4,730 |
Protein-coding | 4,492 |
Software version | 6.7 |
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.
Continue readingQuality 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 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 | 99.01% | 99.01% |
Assembly coverage | 93.49% | 93.49% |
Type assembly coverage | 90.2% | 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_002058745.1 | GCF_002058745.1 | ASM205874v1 | Contig | Mar 21, 2017 |