Genome assembly ASM972953v1
- NCBI RefSeq assembly
- GCF_009729535.1
- Submitted GenBank assembly
- GCA_009729535.1
- Taxon
- Escherichia coli (E. coli)
- Strain
- JP24
- WGS project
- WOFC01
- Submitter
- Federal University of Paraiba (UFPB)
- Date
- Dec 4, 2019
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 5.2 Mb | 5.2 Mb |
Total ungapped length | 5.2 Mb | 5.2 Mb |
Number of contigs | 171 | 171 |
Contig N50 | 101.7 kb | 101.7 kb |
Contig L50 | 15 | 15 |
GC percent | 50.5 | 50.5 |
Genome coverage | 80.0x | 80.0x |
Assembly level | Contig | Contig |
Sample details
- BioSample ID
- SAMN13197356
- Description
- Escherichia coli JP24
- Comment
- not applicable
- Submitter
- Federal University of Paraiba (UFPB)
- Strain
- JP24
- Collected by
- Lara Feital Montezzi
- Collection date
- Oct 20, 2017
- Geographic location
- Brazil: Cabo Branco Beach
- Isolation source
- Coastal Water
- Latitude and longitude
- not applicable
- Culture collection
- not applicable
- Genotype
- not applicable
- Host
- not applicable
- Host age
- not applicable
- Host description
- Coastal Water
- Host disease
- Pathogen: environmental
- Host disease outcome
- not applicable
- Host disease stage
- not applicable
- Host health state
- not applicable
- Host sex
- not applicable
- Host subject id
- not applicable
- Host tissue sampled
- not applicable
- Passage history
- not applicable
- Pathotype
- not applicable
- Serotype
- not applicable
- Serovar
- not applicable
- Specimen voucher
- not applicable
- Subgroup
- not applicable
- Subtype
- not applicable
- Sample name
- ECJP24
- SRA
- SRS5710694
- Models
- Pathogen.env
- Package
- Pathogen.env.1.0
- Submission date
- 2019-11-05T08:44:05.576
- Publication date
- 2019-11-05T00:00:00.000
- Last updated
- 2021-02-24T12:34:40.823
Assembly methods
- Sequencing technology
- Illumina MiSeq
- Comment
Bacteria and source DNA available from Laboratorio de Investigacao em Microbiologia Medica (LIMM), Instituto de Microbiologia Paulo de Goes (IMPG), Bloco I CCS, Universidade Federal do Rio de Janeiro (UFRJ), Ilha do Fundao, Rio de Janeiro RJ, Brazil
The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
- Assembly method
- Unicycler v. 0.4.5
Additional genomes
Browse all Escherichia coli genomes (311944)BioProject
PRJNA587093GenomeTrakr Project: NY State Dept. of Health, Wadsworth Center
Pathogen Detection Resource
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_009729535.1-RS_2024_11_19 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Nov 19, 2024 | Nov 29, 2019 |
Genes | 5,238 | 5,157 |
Protein-coding | 4,965 | 4,971 |
Software version | 6.9 | 4.10 |
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 (v1.2.3)
Completeness: 99.34% (77th Percentile)
Contamination: 1.84%
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Escherichia coli 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
- Escherichia coli
- Submitted species name
- Escherichia coli
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_000010385.1 | GCA_000010385.1 |
Organism name | Escherichia coli SE11 | Escherichia coli |
Type category | claderef | claderef |
ANI | 99.19% | 99.19% |
Assembly coverage | 86.64% | 86.64% |
Type assembly coverage | 87.59% | 87.59% |
Chromosomes
Note: This contig-level genome assembly includes 171 contigs and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_009729535.1 | GCF_009729535.1 | ASM972953v1 | Contig | Dec 4, 2019 |