Genome assembly ASM504579v1
- Taxon
- Escherichia coli (E. coli)
- Strain
- FWSEC0076
- WGS project
- RREV01
- Submitter
- Food and Water Safety Consortium
- Date
- May 1, 2019
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 5 Mb | 5 Mb |
Total ungapped length | 5 Mb | 5 Mb |
Number of chromosomes | 2 | 2 |
Number of scaffolds | 81 | 81 |
Scaffold N50 | 158 kb | 158 kb |
Scaffold L50 | 11 | 11 |
Number of contigs | 81 | 81 |
Contig N50 | 158 kb | 158 kb |
Contig L50 | 11 | 11 |
GC percent | 50.5 | 50.5 |
Genome coverage | 92.0x | 92.0x |
Assembly level | Scaffold | Scaffold |
View sequences | view RefSeq sequences | view GenBank sequences |
Sample details
- BioSample ID
- SAMN08797022
- Description
- Pathogen: clinical or host-associated sample from Escherichia coli
- Comment
- stx2a
- Submitter
- Public Health Agency of Canada
- Collection date
- Apr 4, 2006
- Geographic location
- Canada: Prince Edward Island,Charlottetown
- Collected by
- National Microbiology Laboratory, Public Health Agency of Canada
- Strain
- FWSEC0076
- Serotype
- O1:H20
- Host
- Homo sapiens
- Sample name
- FWSEC0076
- SRA
- SRS3602414
- Models
- Pathogen.cl
- Package
- Pathogen.cl.1.0
- Submission date
- 2018-03-26T16:54:07.016
- Publication date
- 2019-01-23T00:00:00.000
- Last updated
- 2021-02-24T10:56:22.616
Assembly methods
- Sequencing technology
- Illumina GAIIx
- 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/
- Assembly method
- Shovill v. 0.9.0
Additional genomes
Browse all Escherichia coli genomes (311553)BioProject
PRJNA287560Food and Water Safety consortium
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_005045795.1-RS_2024_07_03 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Jul 3, 2024 | Dec 20, 2018 |
Genes | 4,857 | 4,914 |
Protein-coding | 4,604 | 4,681 |
Software version | 6.7 | 4.7 |
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: 99.5% (91st Percentile)
Contamination: 0.52%
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_000350825.1 | GCA_000350825.1 |
Organism name | Escherichia coli KTE26 | Escherichia coli |
Type category | claderef | claderef |
ANI | 98.26% | 98.26% |
Assembly coverage | 89.26% | 89.26% |
Type assembly coverage | 84.88% | 84.88% |
Chromosomes
Note: This scaffold-level genome assembly includes 81 scaffolds and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_005045795.1 | GCF_005045795.1 | ASM504579v1 | Scaffold | May 1, 2019 |