Genome assembly ASM306462v1

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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

RefSeqGenBank
Genome size4.8 Mb4.8 Mb
Total ungapped length4.8 Mb4.8 Mb
Number of contigs5353
Contig N50204.5 kb204.5 kb
Contig L5099
GC percent5252
Genome coverage81.0x81.0x
Assembly levelContigContig
View sequencesview RefSeq sequencesview 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

PRJNA448999

Salmonella enterica subsp. enterica serovar Typhi strain:50_17 Genome sequencing and assembly

Pathogen Detection Resource

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_003064625.1-RS_2024_03_19NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateMar 19, 2024Apr 12, 2018
Genes4,7705,060
Protein-coding4,3154,585
Software version6.74.5

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.

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Quality 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 organismBest match type-strain
Type assemblyGCA_000006945.2GCA_000006945.2
Organism nameSalmonella enterica subsp. enterica serovar Typhimurium str. LT2Salmonella enterica
Type categorytypetype
ANI98.5%98.5%
Assembly coverage89.06%89.06%
Type assembly coverage86.44%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_003064625.1GCF_003064625.1ASM306462v1ContigApr 23, 2018