Genome assembly ASM306462v1
- NCBI RefSeq assembly
- GCF_003064625.1
- Submitted GenBank assembly
- GCA_003064625.1
- Taxon
- Salmonella enterica subsp. enterica serovar Typhi
- Strain
- 50_17
- WGS project
- QAVC01
- Submitter
- Instituto Adolfo Lutz
- Date
- Apr 23, 2018
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 4.8 Mb | 4.8 Mb |
Total ungapped length | 4.8 Mb | 4.8 Mb |
Number of contigs | 53 | 53 |
Contig N50 | 204.5 kb | 204.5 kb |
Contig L50 | 9 | 9 |
GC percent | 52 | 52 |
Genome coverage | 81.0x | 81.0x |
Assembly level | Contig | Contig |
View sequences | view RefSeq sequences | view GenBank sequences |
Sample details
- BioSample ID
- SAMN08875045
- Description
- Pathogen: clinical or host-associated sample from Salmonella enterica subsp. enterica serovar Typhi
- Submitter
- Instituto Adolfo Lutz
- Strain
- 50_17
- Collected by
- Instituto Adolfo Lutz
- Collection date
- 2017
- Geographic location
- Brazil:Sao Paulo
- Host
- Homo sapiens
- Host disease
- typhoid fever
- Isolation source
- blood
- Latitude and longitude
- 23.33 S 46.37 W
- Host age
- 38
- Host sex
- female
- Serovar
- Typhi
- Sub species
- enterica
- Sample name
- BarCode5C5_50_17
- Models
- Pathogen.cl
- Package
- Pathogen.cl.1.0
- Submission date
- 2018-04-06T09:42:07.800
- Publication date
- 2018-04-06T00:00:00.000
- Last updated
- 2018-04-10T14:27:03.929
Assembly methods
- Sequencing technology
- IonTorrent
- 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/
Bacteria and source DNA available from Monique Ribeiro Tiba-Casas, Instituto Adolfo Lutz.
- Assembly method
- SPAdes v. 5.6.0.1
Additional genomes
Browse all Salmonella enterica genomes (581968)BioProject
PRJNA448999Salmonella enterica subsp. enterica serovar Typhi strain:50_17 Genome sequencing and assembly
Pathogen Detection Resource
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_003064625.1-RS_2024_03_19 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Mar 19, 2024 | Apr 12, 2018 |
Genes | 4,770 | 5,060 |
Protein-coding | 4,315 | 4,585 |
Software version | 6.7 | 4.5 |
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: 97.11% (4th Percentile)
Contamination: 0.45%
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 Typhi
- 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 | 98.5% | 98.5% |
Assembly coverage | 89.06% | 89.06% |
Type assembly coverage | 86.44% | 86.44% |
Chromosomes
Note: This contig-level genome assembly includes 53 contigs and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_003064625.1 | GCF_003064625.1 | ASM306462v1 | Contig | Apr 23, 2018 |