Genome assembly ASM152009v1
- NCBI RefSeq assembly
- GCF_001520095.1 (suppressed)
- Submitted GenBank assembly
- GCA_001520095.1
- Taxon
- Escherichia coli (E. coli)
- Strain
- GN02620
- WGS project
- LQUT01
- Submitter
- JCVI
- Date
- Jan 20, 2016
Genome notes
NCBI has noted the following for this genome assembly. View definitions
- annotation fails completeness check
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 5 Mb | 5 Mb |
Total ungapped length | 5 Mb | 5 Mb |
Number of contigs | 303 | 303 |
Contig N50 | 34.4 kb | 34.4 kb |
Contig L50 | 46 | 46 |
GC percent | 51 | 51 |
Genome coverage | 131.2x | 131.2x |
Assembly level | Contig | Contig |
View sequences | view GenBank sequences |
Sample details
- BioSample ID
- SAMN03922949
- Description
- Sample of Escherichia coli GN02620
- Comment
- Sample of Escherichia coli GN02620
- Submitter
- JCVI
- Strain
- GN02620
- Collected by
- Vance Fowler
- Collection date
- 2007
- Geographic location
- USA
- Host
- Homo sapiens
- Host disease
- Bloodstream infection
- Isolation source
- bodily fluid
- Latitude and longitude
- 36 N 78.9 W
- Host health state
- Diseased
- SRA
- SRS1246421
- JCVI
- GCID_ECOLID_00093
- Models
- Pathogen.cl
- Package
- Pathogen.cl.1.0
- Submission date
- 2015-07-24T16:41:30.000
- Publication date
- 2015-07-24T00:00:00.000
- Last updated
- 2019-05-23T15:39:53.333
Assembly methods
- Sequencing technology
- Illumina NextSeq 500
- 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
- SPAdes v. 3.1.1
Additional genomes
Browse all Escherichia coli genomes (312327)BioProject
PRJNA290784Genomic sequencing of Escherichia coli bloodstream isolates
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | May 23, 2023 | Jan 12, 2016 |
Genes | 5,266 | 5,224 |
Protein-coding | 4,683 | 4,762 |
Software version | 6.5 | 3.1 |
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 (v1.2.2)
Completeness: 95.48% (2nd Percentile)
Contamination: 0.89%
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_024519395.1 | GCA_024519395.1 |
Organism name | Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775 | Escherichia coli |
Type category | neotype | neotype |
ANI | 99.89% | 99.89% |
Assembly coverage | 97.43% | 97.43% |
Type assembly coverage | 91.16% | 91.16% |
Chromosomes
Note: This contig-level genome assembly includes 303 contigs and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_001520095.1 | GCF_001520095.1 | ASM152009v1 | Contig | Jan 20, 2016 |