Genome assembly ASM623426v1
- NCBI RefSeq assembly
- GCF_006234265.1
- Submitted GenBank assembly
- GCA_006234265.1
- Taxon
- Escherichia coli (E. coli)
- Strain
- NOR2_60
- WGS project
- SQFY01
- Submitter
- University of Tartu
- Date
- Jun 11, 2019
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 5.1 Mb | 5.1 Mb |
Total ungapped length | 5.1 Mb | 5.1 Mb |
Number of scaffolds | 105 | 105 |
Scaffold N50 | 266.5 kb | 266.5 kb |
Scaffold L50 | 7 | 7 |
Number of contigs | 226 | 226 |
Contig N50 | 81.2 kb | 81.2 kb |
Contig L50 | 21 | 21 |
GC percent | 51 | 51 |
Genome coverage | 83.1x | 83.1x |
Assembly level | Scaffold | Scaffold |
Sample details
- BioSample ID
- SAMN11232906
- Description
- Pathogen: clinical or host-associated sample from Escherichia coli
- Submitter
- University of Tartu
- Strain
- NOR2_60
- Collected by
- Baltic ESBL Project
- Collection date
- 2012
- Geographic location
- Norway
- Host
- Homo sapiens
- Isolation source
- clinical sample
- Sample name
- NOR2_60
- Models
- Pathogen.cl
- Package
- Pathogen.cl.1.0
- Submission date
- 2019-03-22T09:33:17.290
- Publication date
- 2019-03-22T00:00:00.000
- Last updated
- 2019-03-22T09:33:17.290
Assembly methods
- Sequencing technology
- HiSeq2500 Rapid Run
- Assembly method
- Velvet v. 1.2.10
Additional genomes
Browse all Escherichia coli genomes (311553)BioProject
PRJNA528606Escherichia coli Genome sequencing and assembly
Annotation details
RefSeq | |
---|---|
Provider | NCBI RefSeq |
Name | GCF_006234265.1-RS_2024_07_09 |
Date | Jul 9, 2024 |
Genes | 5,127 |
Protein-coding | 4,823 |
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 (v1.2.3)
Completeness: 99.02% (54th Percentile)
Contamination: 0.75%
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 | 99.9% | 99.9% |
Assembly coverage | 98.27% | 98.27% |
Type assembly coverage | 93.91% | 93.91% |
Chromosomes
Note: This scaffold-level genome assembly includes 105 scaffolds and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_006234265.1 | GCF_006234265.1 | ASM623426v1 | Scaffold | Jun 11, 2019 |