Genome assembly PDT002466010.1
- Submitted GenBank assembly
- GCA_044905865.1
- Taxon
- Escherichia coli UTI89
- Strain
- ECOL-24-VL-NY-FL-0009
- WGS project
- ABWJLH01
- Submitter
- Vet-LIRN-CVM-FDA
- Date
- Nov 14, 2024
Genome notes
NCBI has noted the following for this genome assembly. View definitions
- from large multi-isolate project
Assembly statistics
GenBank | |
---|---|
Genome size | 5.2 Mb |
Total ungapped length | 5.2 Mb |
Number of contigs | 50 |
Contig N50 | 540.3 kb |
Contig L50 | 4 |
GC percent | 50.5 |
Genome coverage | 177.0x |
Assembly level | Contig |
Sample details
- BioSample ID
- SAMN44733941
- Description
- One Health Enteric sample from Escherichia coli UTI89
- Submitter
- Vet-LIRN: Cornell University, Ithaca, NY
- Strain
- ECOL-24-VL-NY-FL-0009
- Collected by
- Florida Department of Agriculture and Consumer Services; Bronson Animal Disease Diagnostic Laboratory
- Collection date
- Apr 16, 2024
- Geographic location
- USA:FL
- Isolation source
- urine
- Source type
- animal
- Purpose of sampling
- Monitoring (AMR project)
- Host
- Canis lupus familiaris
- Host disease
- Infection
- Intended consumer
- not applicable
- Project name
- Vet-LIRN
- Sequenced by
- WGS-NY
- Sample name
- ECOL-24-VL-NY-FL-0009
- SRA
- SRS23214111
- Models
- One Health Enteric
- Package
- OneHealthEnteric.1.0
- Submission date
- 2024-11-14T07:17:04.600
- Publication date
- 2024-11-14T00:00:00.000
- Last updated
- 2024-11-14T07:24:28.270
Assembly methods
- Sequencing technology
- ILLUMINA
- Comment
The annotation was added by the assembly submitters using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about stand-alone PGAP can be found here: https://github.com/ncbi/pgap/
This draft WGS assembly was generated by running SKESA to generate a de-novo assembly. The de-novo assembly was then concatenated with contigs generated using a guided assembler using antimicrobial resistance genes as baits to comprehensively catalog the set of resistance genes in the isolate. Note, some parts of the contigs derived from the guided assembler may overlap de-novo contigs, and other guided assembler contigs. De-novo contigs can be differentiated from guided assembler contigs by their names , which include either 'denovo' or 'guided'.
- Assembly method
- SKESA v. 2.2
Additional genomes
Browse all Escherichia coli genomes (311944)BioProject
PRJNA324565Vet-LIRN-E.coli-NY
Pathogen Detection Resource
Annotation details
GenBank | |
---|---|
Provider | NCBI |
Name | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Nov 14, 2024 |
Genes | 5,069 |
Protein-coding | 4,761 |
Software version | 2024-07-18.build7555 |
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
Taxonomy check
- Taxonomy check status
- OK
- Best match status
- species_match
- Submitted organism name
- Escherichia coli UTI89
- 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_000013265.1 | GCA_000013265.1 |
Organism name | Escherichia coli UTI89 | Escherichia coli |
Type category | claderef | claderef |
ANI | 99.08% | 99.08% |
Assembly coverage | 88.79% | 88.79% |
Type assembly coverage | 88.95% | 88.95% |
Chromosomes
Note: This contig-level genome assembly includes 50 contigs and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_044905865.1 | n/a | PDT002466010.1 | Contig | Nov 14, 2024 |