Genome assembly ASM4503257v1
- NCBI RefSeq assembly
- GCF_045032575.1
- Submitted GenBank assembly
- GCA_045032575.1
- Taxon
- Escherichia coli (E. coli)
- Strain
- BD_EC_CHK_04
- WGS project
- JBJGAA01
- Submitter
- Department of Genetics and Animal Breeding, Chattogram Veterinary and Animal Sciences University
- Date
- Nov 18, 2024
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 5.2 Mb | 5.2 Mb |
Total ungapped length | 5.2 Mb | 5.2 Mb |
Number of contigs | 293 | 293 |
Contig N50 | 150.3 kb | 150.3 kb |
Contig L50 | 11 | 11 |
GC percent | 50.5 | 50.5 |
Genome coverage | 288.0x | 288.0x |
Assembly level | Contig | Contig |
View sequences | view RefSeq sequences |
Sample details
- BioSample ID
- SAMN40074346
- Description
- E coli chicken 04
- Submitter
- Department of Genetics and Animal Breeding, Chattogram Veterinary and Animal Sciences University
- Strain
- BD_EC_CHK_04
- Genotype
- ST38
- Collected by
- DR Mishuk Shaha
- Collection date
- Oct 28, 2023
- Geographic location
- Bangladesh:Chattogram
- Isolation source
- cloacal swab
- Source type
- animal
- Purpose of sampling
- Isolation of multidrug resistance Escherichia coli from chicken
- Host
- Chicken
- Animal environment
- House-hold
- Sample name
- BD_EC_CHK_04
- SRA
- SRS20640563
- Models
- One Health Enteric
- Package
- OneHealthEnteric.1.0
- Submission date
- 2024-02-23T09:57:04.683
- Publication date
- 2024-07-01T00:00:00.000
- Last updated
- 2024-11-13T14:24:23.899
Assembly methods
- Sequencing technology
- Illumina NextSeq
- Comment
- 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
- Spades v. 3.15.5
Additional genomes
Browse all Escherichia coli genomes (311916)BioProject
PRJNA1072078Escherichia coli Genome sequencing
Pathogen Detection Resource
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_045032575.1-RS_2024_11_20 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Nov 20, 2024 | Nov 13, 2024 |
Genes | 5,189 | 5,190 |
Protein-coding | 4,876 | 4,955 |
Software version | 6.9 | 6.8 |
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: 99.5% (91st Percentile)
Contamination: 0.48%
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_000350825.1 | GCA_000350825.1 |
Organism name | Escherichia coli KTE26 | Escherichia coli |
Type category | claderef | claderef |
ANI | 98.34% | 98.34% |
Assembly coverage | 85.87% | 85.87% |
Type assembly coverage | 84.7% | 84.7% |
Chromosomes
Note: This contig-level genome assembly includes 293 contigs and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_045032575.1 | GCF_045032575.1 | ASM4503257v1 | Contig | Nov 18, 2024 |