Genome assembly ASM517109v1
- 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
RefSeq | GenBank | |
---|---|---|
Genome size | 5.3 Mb | 5.3 Mb |
Total ungapped length | 5.3 Mb | 5.3 Mb |
Number of chromosomes | 3 | 3 |
Number of scaffolds | 6 | 6 |
Scaffold N50 | 5.1 Mb | 5.1 Mb |
Scaffold L50 | 1 | 1 |
Number of contigs | 6 | 6 |
Contig N50 | 5.1 Mb | 5.1 Mb |
Contig L50 | 1 | 1 |
GC percent | 51 | 51 |
Assembly level | Chromosome | Chromosome |
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
PRJNA287560Food and Water Safety consortium
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_005171095.1-RS_2024_06_19 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Jun 19, 2024 | Aug 28, 2018 |
Genes | 5,217 | 5,550 |
Protein-coding | 4,894 | 5,173 |
Software version | 6.7 | 4.6 |
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 readingQuality 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 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 | 99.16% | 99.16% |
Assembly coverage | 85.12% | 85.12% |
Type assembly coverage | 87.74% | 87.74% |
Chromosomes
Chromosome | GenBank | RefSeq | Size (bp) | GC content (%) | Unlocalized count | Action |
---|---|---|---|---|---|---|
chromosome | CP031892.1 | NZ_CP031892.1 | 5,064,577 | 51 | 0 | |
unnamed1 | CP031893.1 | NZ_CP031893.1 | 134,626 | 50.5 | 0 |
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_005171095.1 | GCF_005171095.1 | ASM517109v1 | Chromosome | May 1, 2019 |