Genome assembly ASM222829v1
- NCBI RefSeq assembly
- GCF_002228295.1
- Submitted GenBank assembly
- GCA_002228295.1
- Taxon
- Escherichia coli (E. coli)
- Strain
- MOD1-EC5567
- WGS project
- NLLG01
- Submitter
- FDA/CFSAN
- Date
- Jul 25, 2017
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 5.2 Mb | 5.2 Mb |
Total ungapped length | 5.2 Mb | 5.2 Mb |
Number of contigs | 371 | 371 |
Contig N50 | 52.9 kb | 52.9 kb |
Contig L50 | 27 | 27 |
GC percent | 50.5 | 50.5 |
Genome coverage | 97.3x | 97.3x |
Assembly level | Contig | Contig |
View sequences | view RefSeq sequences | view GenBank sequences |
Sample details
- BioSample ID
- SAMN05440372
- Description
- Pathogen: environmental/food/other sample from Escherichia coli
- Submitter
- FDA Center for Food Safety and Applied Nutrition
- Isolate name alias
- CFSAN049813,C-B-09-2-2-M-10
- Strain
- MOD1-EC5567
- Attribute package
- environmental/food/other
- Isolation source
- chicken feces
- Ontological term
- chicken:FOODON_03411457| feces:UBERON_0001988| gallus gallus:NCBITAXON_9031
- Interagency Food Safety Analytics Collaboration (IFSAC) category
- veterinary clinical/research| chicken
- Source type
- animal
- Collection date
- Apr 24, 1979
- Geographic location
- USA
- Host
- Gallus gallus
- Collected by
- Pennsylvania State University| Escherichia coli Reference Center
- Food product origin geographic location
- USA:CO
- Project name
- GenomeTrakr
- Sequenced by
- Pennsylvania State University| Escherichia coli Reference Center
- SRA
- SRS1594172
- CFSAN
- CFSAN049813
- Models
- Pathogen.env
- Package
- Pathogen.env.1.0
- Submission date
- 2016-07-26T09:11:15.613
- Publication date
- 2016-07-26T00:00:00.000
- Last updated
- 2024-08-08T11:39:09.071
Assembly methods
- Sequencing technology
- Illumina NextSeq 500
- Assembly method
- SPAdes v. 3.8.2
Additional genomes
Browse all Escherichia coli genomes (311553)BioProject
PRJNA230969GenomeTrakr Project: US Food and Drug Administration
Pathogen Detection Resource
Annotation details
RefSeq | |
---|---|
Provider | NCBI RefSeq |
Name | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Feb 4, 2024 |
Genes | 5,455 |
Protein-coding | 5,022 |
Software version | 6.6 |
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: 97.46% (7th Percentile)
Contamination: 0.39%
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_000210475.1 | GCA_000210475.1 |
Organism name | Escherichia coli ETEC H10407 | Escherichia coli |
Type category | claderef | claderef |
ANI | 98.98% | 98.98% |
Assembly coverage | 84.52% | 84.52% |
Type assembly coverage | 83% | 83% |
Chromosomes
Note: This contig-level genome assembly includes 371 contigs and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_002228295.1 | GCF_002228295.1 | ASM222829v1 | Contig | Jul 25, 2017 |