Genome assembly ASM2038158v1
- NCBI RefSeq assembly
- GCF_020381585.1
- Submitted GenBank assembly
- GCA_020381585.1
- Taxon
- Escherichia coli (E. coli)
- Strain
- CX13
- WGS project
- JAGTID01
- Submitter
- Agriculture & Agri-Food Canada
- Date
- Oct 8, 2021
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 4.6 Mb | 4.6 Mb |
Total ungapped length | 4.6 Mb | 4.6 Mb |
Number of contigs | 48 | 48 |
Contig N50 | 268.7 kb | 268.7 kb |
Contig L50 | 7 | 7 |
GC percent | 50.5 | 50.5 |
Genome coverage | 188.0x | 188.0x |
Assembly level | Contig | Contig |
View sequences | view RefSeq sequences |
Sample details
- BioSample ID
- SAMN18824009
- Description
- MIGS Cultured Bacterial/Archaeal sample from Escherichia coli
- Comment
- Keywords: GSC:MIxS;MIGS:6.0
- Submitter
- Agriculture & Agri-Food Canada
- Strain
- CX13
- Collection date
- 2014/2015
- Broad-scale environmental context
- meat_39
- Local-scale environmental context
- not collected
- Environmental medium
- not collected
- Geographic location
- Canada: Alberta
- Isolation and growth condition
- not applicable
- Latitude and longitude
- not collected
- Number of replicons
- not collected
- Reference for biomaterial
- not applicable
- Depth
- not applicable
- Sample name
- CX13
- SRA
- SRS8791714
- Models
- MIGS.ba, MIGS/MIMS/MIMARKS.miscellaneous
- Package
- MIGS.ba.miscellaneous.6.0
- Submission date
- 2021-04-21T16:42:04.867
- Publication date
- 2021-10-09T18:39:36.290
- Last updated
- 2021-10-09T18:39:36.290
Assembly methods
- Sequencing technology
- Illumina HiSeq
- Comment
- The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
- Assembly method
- SPAdes v. 3.13.1
Additional genomes
Browse all Escherichia coli genomes (312504)BioProject
PRJNA716667Genetic characterization of Escherichia coli in meat that harbor locus of heat resistance
Pathogen Detection Resource
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Nov 15, 2023 | Apr 22, 2021 |
Genes | 4,522 | 4,470 |
Protein-coding | 4,271 | 4,255 |
Software version | 6.6 | 5.1 |
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: 99.46% (88th Percentile)
Contamination: 0.56%
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_000010385.1 | GCA_000010385.1 |
Organism name | Escherichia coli SE11 | Escherichia coli |
Type category | claderef | claderef |
ANI | 99.3% | 99.3% |
Assembly coverage | 93.48% | 93.48% |
Type assembly coverage | 84.12% | 84.12% |
Chromosomes
Note: This contig-level genome assembly includes 48 contigs and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_020381585.1 | GCF_020381585.1 | ASM2038158v1 | Contig | Oct 8, 2021 |