Genome assembly ASM213440v1

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NCBI RefSeq assembly
GCF_002134405.1
Submitted GenBank assembly
GCA_002134405.1
Taxon
Escherichia coli (E. coli)
Strain
OLC1062
WGS project
NENB01
Submitter
Canadian Food Inspection Agency
Date
May 12, 2017

Assembly statistics

RefSeqGenBank
Genome size5.1 Mb5.1 Mb
Total ungapped length5.1 Mb5.1 Mb
Number of contigs167167
Contig N50135.5 kb135.5 kb
Contig L501313
GC percent50.550.5
Genome coverage50.1x50.1x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN04420151
Description
CA_CFIA-737
Submitter
Canadian Food Inspection Agency
Genotype
vtx1a
Serotype
O103:H2
Geographic location
Canada
SeqID
2014-SEQ-0254
Isolation source
not applicable
Sample type
cell culture
Collection date
Dec 21, 2012
Strain
OLC1062
Sample name
CA_CFIA-737
SRA
SRS2532439
Models
Microbe, viral or environmental
Package
Microbe.1.0
Submission date
2016-01-18T11:59:06.733
Publication date
2016-01-18T11:59:02.667
Last updated
2017-09-22T15:12:18.767

Assembly methods

Sequencing technology
Illumina MiSeq
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/

Source DNA available from Burton Blais, 960 Carling Ave., Bldg. 22, Ottawa, Ontario, Canada, K1A 0C6

Assembly method
SPAdes v. 3.7.1

Additional genomes

Browse all Escherichia coli genomes (312255)

BioProject

PRJNA309770

Application of genomics in the determination of verotoxigenic Escherichia coli toxin subtypes

Pathogen Detection Resource

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_002134405.1-RS_2024_07_06NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateJul 6, 2024Apr 26, 2017
Genes5,2625,563
Protein-coding4,8915,209
Software version6.74.1

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: 99.4% (83rd Percentile)

Contamination: 0.21%

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
ANI99.1%99.1%
Assembly coverage87.66%87.66%
Type assembly coverage87.52%87.52%

Chromosomes

Note: This contig-level genome assembly includes 167 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_002134405.1GCF_002134405.1ASM213440v1ContigMay 12, 2017