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Genome assembly ASM504579v1

Actions
Taxon
Escherichia coli (E. coli)
Strain
FWSEC0076
WGS project
RREV01
Submitter
Food and Water Safety Consortium
Date
May 1, 2019

Assembly statistics

RefSeqGenBank
Genome size5 Mb5 Mb
Total ungapped length5 Mb5 Mb
Number of chromosomes22
Number of scaffolds8181
Scaffold N50158 kb158 kb
Scaffold L501111
Number of contigs8181
Contig N50158 kb158 kb
Contig L501111
GC percent50.550.5
Genome coverage92.0x92.0x
Assembly levelScaffoldScaffold
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN08797022
Description
Pathogen: clinical or host-associated sample from Escherichia coli
Comment
stx2a
Submitter
Public Health Agency of Canada
Collection date
Apr 4, 2006
Geographic location
Canada: Prince Edward Island,Charlottetown
Collected by
National Microbiology Laboratory, Public Health Agency of Canada
Strain
FWSEC0076
Serotype
O1:H20
Host
Homo sapiens
Sample name
FWSEC0076
SRA
SRS3602414
Models
Pathogen.cl
Package
Pathogen.cl.1.0
Submission date
2018-03-26T16:54:07.016
Publication date
2019-01-23T00:00:00.000
Last updated
2021-02-24T10:56:22.616

Assembly methods

Sequencing technology
Illumina GAIIx
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/
Assembly method
Shovill v. 0.9.0

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_005045795.1-RS_2024_07_03NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateJul 3, 2024Dec 20, 2018
Genes4,8574,914
Protein-coding4,6044,681
Software version6.74.7

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: 0.52%

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
ANI98.26%98.26%
Assembly coverage89.26%89.26%
Type assembly coverage84.88%84.88%

Chromosomes

Note: This scaffold-level genome assembly includes 81 scaffolds and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_005045795.1GCF_005045795.1ASM504579v1ScaffoldMay 1, 2019