Genome assembly ASM296529v1
- NCBI RefSeq assembly
- GCF_002965295.1
- Submitted GenBank assembly
- GCA_002965295.1
- Taxon
- Escherichia sp. MOD1-EC5949
- Strain
- MOD1-EC5949
- WGS project
- PTSS01
- Submitter
- FDA/CFSAN
- Date
- Feb 28, 2018
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 4.7 Mb | 4.7 Mb |
Total ungapped length | 4.7 Mb | 4.7 Mb |
Number of contigs | 127 | 127 |
Contig N50 | 151.2 kb | 151.2 kb |
Contig L50 | 10 | 10 |
GC percent | 50.5 | 50.5 |
Genome coverage | 28.7x | 28.7x |
Assembly level | Contig | Contig |
View sequences | view RefSeq sequences | view GenBank sequences |
Sample details
- BioSample ID
- SAMN05439388
- Description
- Pathogen: environmental/food/other sample from Escherichia sp.
- Submitter
- FDA Center for Food Safety and Applied Nutrition
- Isolation source
- feces
- Collected by
- Penn State E. coli Reference Center
- Strain
- MOD1-EC5949
- Geographic location
- USA:AK
- Collection date
- Jul 30, 2008
- Isolate name alias
- CFSAN044186, 807160033
- Attribute package
- clinical/host-associated
- Host
- Anas platyrhynchos
- Genotype
- cryptic lineage 5
- SRA
- SRS1592793
- CFSAN
- CFSAN044186
- Models
- Pathogen.env
- Package
- Pathogen.env.1.0
- Submission date
- 2016-07-25T16:42:03.916
- Publication date
- 2016-07-25T00:00:00.000
- Last updated
- 2021-02-10T11:21:37.949
Assembly methods
- Sequencing technology
- Illumina NextSeq 500
- Assembly method
- SPAdes v. 3.8.2
Additional genomes
Browse all Escherichia sp. MOD1-EC5949 genomes (1)BioProject
PRJNA230969GenomeTrakr Project: US Food and Drug Administration
Annotation details
RefSeq | |
---|---|
Provider | NCBI RefSeq |
Name | GCF_002965295.1-RS_2024_03_14 |
Date | Mar 14, 2024 |
Genes | 4,724 |
Protein-coding | 4,422 |
Software version | 6.7 |
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 (v1.2.2)
Completeness: 95.79% (100th Percentile)
Contamination: 0.1%
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Escherichia CheckM marker set. For more information on CheckM, see Parks, et al. Genome Res (2015).
Taxonomy check
- Taxonomy check status
- OK
- Best match status
- genus_match
- Submitted organism name
- Escherichia sp. MOD1_EC5949
- Submitted species name
- Escherichia sp. MOD1_EC5949
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | n/a | GCA_002900365.1 |
Organism name | n/a | Escherichia marmotae |
Type category | n/a | type |
ANI | n/a | 99.31% |
Assembly coverage | n/a | 84.35% |
Type assembly coverage | n/a | 81.36% |
Chromosomes
Note: This contig-level genome assembly includes 127 contigs and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_002965295.1 | GCF_002965295.1 | ASM296529v1 | Contig | Feb 28, 2018 |