Genome assembly ASM972953v1

Actions
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

RefSeqGenBank
Genome size5.2 Mb5.2 Mb
Total ungapped length5.2 Mb5.2 Mb
Number of contigs171171
Contig N50101.7 kb101.7 kb
Contig L501515
GC percent50.550.5
Genome coverage80.0x80.0x
Assembly levelContigContig

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

PRJNA587093

GenomeTrakr Project: NY State Dept. of Health, Wadsworth Center

Pathogen Detection Resource

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_009729535.1-RS_2024_11_19NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateNov 19, 2024Nov 29, 2019
Genes5,2385,157
Protein-coding4,9654,971
Software version6.94.10

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 reading

Quality 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 organismBest match type-strain
Type assemblyGCA_000010385.1GCA_000010385.1
Organism nameEscherichia coli SE11Escherichia coli
Type categorycladerefcladeref
ANI99.19%99.19%
Assembly coverage86.64%86.64%
Type assembly coverage87.59%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_009729535.1GCF_009729535.1ASM972953v1ContigDec 4, 2019