Genome assembly ASM2038158v1

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NCBI RefSeq assembly
GCF_020381585.1
Submitted GenBank assembly
GCA_020381585.1
Taxon
Escherichia coli (E. coli)
Strain
CX13
WGS project
JAGTID01
Submitter
Agriculture & Agri-Food Canada
Date
Oct 8, 2021

Assembly statistics

RefSeqGenBank
Genome size4.6 Mb4.6 Mb
Total ungapped length4.6 Mb4.6 Mb
Number of contigs4848
Contig N50268.7 kb268.7 kb
Contig L5077
GC percent50.550.5
Genome coverage188.0x188.0x
Assembly levelContigContig
View sequencesview RefSeq sequences

Sample details

BioSample ID
SAMN18824009
Description
MIGS Cultured Bacterial/Archaeal sample from Escherichia coli
Comment
Keywords: GSC:MIxS;MIGS:6.0
Submitter
Agriculture & Agri-Food Canada
Strain
CX13
Collection date
2014/2015
Broad-scale environmental context
meat_39
Local-scale environmental context
not collected
Environmental medium
not collected
Geographic location
Canada: Alberta
Isolation and growth condition
not applicable
Latitude and longitude
not collected
Number of replicons
not collected
Reference for biomaterial
not applicable
Depth
not applicable
Sample name
CX13
SRA
SRS8791714
Models
MIGS.ba, MIGS/MIMS/MIMARKS.miscellaneous
Package
MIGS.ba.miscellaneous.6.0
Submission date
2021-04-21T16:42:04.867
Publication date
2021-10-09T18:39:36.290
Last updated
2021-10-09T18:39:36.290

Assembly methods

Sequencing technology
Illumina HiSeq
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. 3.13.1

Additional genomes

Browse all Escherichia coli genomes (312504)

BioProject

PRJNA716667

Genetic characterization of Escherichia coli in meat that harbor locus of heat resistance

Pathogen Detection Resource

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateNov 15, 2023Apr 22, 2021
Genes4,5224,470
Protein-coding4,2714,255
Software version6.65.1

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 (v1.2.2)

Completeness: 99.46% (88th Percentile)

Contamination: 0.56%

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
ANI99.3%99.3%
Assembly coverage93.48%93.48%
Type assembly coverage84.12%84.12%

Chromosomes

Note: This contig-level genome assembly includes 48 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_020381585.1GCF_020381585.1ASM2038158v1ContigOct 8, 2021