Genome assembly ASM213440v1
- 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
RefSeq | GenBank | |
---|---|---|
Genome size | 5.1 Mb | 5.1 Mb |
Total ungapped length | 5.1 Mb | 5.1 Mb |
Number of contigs | 167 | 167 |
Contig N50 | 135.5 kb | 135.5 kb |
Contig L50 | 13 | 13 |
GC percent | 50.5 | 50.5 |
Genome coverage | 50.1x | 50.1x |
Assembly level | Contig | Contig |
View sequences | view RefSeq sequences | view 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
PRJNA309770Application of genomics in the determination of verotoxigenic Escherichia coli toxin subtypes
Pathogen Detection Resource
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_002134405.1-RS_2024_07_06 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Jul 6, 2024 | Apr 26, 2017 |
Genes | 5,262 | 5,563 |
Protein-coding | 4,891 | 5,209 |
Software version | 6.7 | 4.1 |
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 readingQuality 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 organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_000010385.1 | GCA_000010385.1 |
Organism name | Escherichia coli SE11 | Escherichia coli |
Type category | claderef | claderef |
ANI | 99.1% | 99.1% |
Assembly coverage | 87.66% | 87.66% |
Type assembly coverage | 87.52% | 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_002134405.1 | GCF_002134405.1 | ASM213440v1 | Contig | May 12, 2017 |