Full information on isolate 2020/00048 (id:9075)
Projects
This isolate is a member of the following project:
- Public isolates
- This project contains the isolates that should be publicly available through the public access database.
Provenance/primary metadata
- id
- 9075
- isolate
- 2020/00048
- alias
- IP43181
- species genotypic
- enterocolitica
- genotype
- 4
- category
- Veterinary
- origin
- Tonsil
- host
- pig
- sender
- Sylvie Brémont, Institut Pasteur, Paris
- curator
- Cyril Savin, Institut Pasteur, Paris, France (E-mail: cyril.savin@pasteur.fr)
- update history
- 14 updates show details
- date entered
- 2020-01-23
- datestamp
- 2024-07-01
- country
- Costa Rica
Publication (1)
- Savin C, Oropeza G, Barboza Fallas LA, Rivas-Solano O, Chanto G, Pizarro-Cerdá J (2025). Genomic Characterization of Yersinia enterocolitica Isolates, Costa Rica. Emerg Infect Dis 31:848-860
Sequence bin
- method
- Illumina
- contigs
- 172
- total length
- 4,336,642 bp
- max length
- 178,232 bp
- mean length
- 25,214 bp
- N50
- 49,619
- L50
- 31
- N90
- 13,277
- L90
- 95
- N95
- 9,382
- L95
- 114
- %GC
- 47.10
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,789
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| Yersinia cgMLST | 500 | 498 | 99 | |
| Y.enterocolitica cgMLST | 1727 | 1724 | 99 | |
| Y.pseudotuberculosis cgMLST | 1921 | 498 | 25 | |
Similar isolates (determined by classification schemes)
Experimental schemes are subject to change and are not a stable part of the nomenclature.
| Classification scheme | Underlying scheme | Clustering method | Mismatch threshold | Status | Group |
|---|---|---|---|---|---|
| Y.enterocolitica_3-mismatch | Y.enterocolitica cgMLST | Single-linkage | 3 | experimental | 3972 (2 isolates) |
| Y.enterocolitica_5-mismatch | Y.enterocolitica cgMLST | Single-linkage | 5 | experimental | 3151 (3 isolates) |
| Y.enterocolitica_3-mismatch | Y.enterocolitica cgMLST | Single-linkage | 3 | experimental | 3972 (2 isolates) |
| Y.enterocolitica_5-mismatch | Y.enterocolitica cgMLST | Single-linkage | 5 | experimental | 3151 (3 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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