Genome assembly ASM4503257v1

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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

RefSeqGenBank
Genome size5.2 Mb5.2 Mb
Total ungapped length5.2 Mb5.2 Mb
Number of contigs293293
Contig N50150.3 kb150.3 kb
Contig L501111
GC percent50.550.5
Genome coverage288.0x288.0x
Assembly levelContigContig
View sequencesview 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

PRJNA1072078

Escherichia coli Genome sequencing

Pathogen Detection Resource

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_045032575.1-RS_2024_11_20NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateNov 20, 2024Nov 13, 2024
Genes5,1895,190
Protein-coding4,8764,955
Software version6.96.8

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 reading

Quality 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 organismBest match type-strain
Type assemblyGCA_000350825.1GCA_000350825.1
Organism nameEscherichia coli KTE26Escherichia coli
Type categorycladerefcladeref
ANI98.34%98.34%
Assembly coverage85.87%85.87%
Type assembly coverage84.7%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_045032575.1GCF_045032575.1ASM4503257v1ContigNov 18, 2024