Genome assembly ASM517109v1

Actions
NCBI RefSeq assembly
GCF_005171095.1
Submitted GenBank assembly
GCA_005171095.1
Taxon
Escherichia coli O113:H21
Strain
FWSEC0011
Submitter
Food and Water Safety Consortium
Date
May 1, 2019

Assembly statistics

RefSeqGenBank
Genome size5.3 Mb5.3 Mb
Total ungapped length5.3 Mb5.3 Mb
Number of chromosomes33
Number of scaffolds66
Scaffold N505.1 Mb5.1 Mb
Scaffold L5011
Number of contigs66
Contig N505.1 Mb5.1 Mb
Contig L5011
GC percent5151
Assembly levelChromosomeChromosome

Sample details

BioSample ID
SAMN08768112
Description
Pathogen: environmental/food/other sample from Escherichia coli O113:H21
Comment
stx2d
Submitter
NML_bioinformatics
Collection date
2004
Geographic location
Canada:Ontario
Collected by
Laboratory for Foodborne Zoonoses: Public Health Agency of Canada
Strain
FWSEC0011
Serotype
O113:H21
Isolation source
Domesticated, Livestock: Bovine: animal manure: agricultural - farm
Host
bovine
Sample name
FWSEC0011
SRA
SRS3815841
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2018-03-21T16:24:05.526
Publication date
2019-01-23T00:00:00.000
Last updated
2019-05-01T13:34:33.555

Assembly methods

Sequencing technology
Illumina MiSeq;Oxford Nanopore MinION
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
Unicycler;Canu v. 0.4.4.0;1.7

BioProject

PRJNA287560

Food and Water Safety consortium

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_005171095.1-RS_2024_06_19NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateJun 19, 2024Aug 28, 2018
Genes5,2175,550
Protein-coding4,8945,173
Software version6.74.6

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: 99.53% (95th Percentile)

Contamination: 0.83%

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 O113:H21
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
ANI99.16%99.16%
Assembly coverage85.12%85.12%
Type assembly coverage87.74%87.74%

Chromosomes

Chromosome
GenBank
RefSeq
Size (bp)
GC content (%)
Unlocalized count
Action
chromosomeCP031892.1NZ_CP031892.15,064,577510
unnamed1CP031893.1NZ_CP031893.1134,62650.50

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_005171095.1GCF_005171095.1ASM517109v1ChromosomeMay 1, 2019