Full information on isolate IP38274 (id:2133)
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
- 2133
- isolate
- IP38274
- accession number
- GCA_902169545.1
- species phenotypic
- enterocolitica
- biotype
- 2
- serotype
- O:9
- species genotypic
- enterocolitica
- genotype
- 2/3-9b
- isolation date
- 10/09/2016
- category
- Clinical
- origin
- Feces
- age
- 3
- sex
- M
- comments
- jusqu'au 12/05/2019 assignation: Y.enterocolitica genotype 23-9b
- sender
- Cyril Savin
- curator
- Cyril Savin, Institut Pasteur, Paris, France (E-mail: cyril.savin@pasteur.fr)
- update history
- 18 updates show details
- date entered
- 2017-01-12
- datestamp
- 2026-01-05
- date received
- 2016-09-14
- CP patient
- 12450
- CP labo
- 12000
- country code
- FRA
- country
- France
Sequence bin
- method
- Unknown
- contigs
- 215
- total length
- 4,555,039 bp
- max length
- 154,588 bp
- mean length
- 21,187 bp
- N50
- 58,034
- L50
- 26
- N90
- 12,854
- L90
- 85
- N95
- 7,064
- L95
- 109
- %GC
- 46.92
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,835
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 | 500 | 100 | |
| Y.enterocolitica cgMLST | 1727 | 1722 | 99 | |
| Y.pseudotuberculosis cgMLST | 1921 | 500 | 26 | |
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 | 5062 (51 isolates) |
| Y.enterocolitica_5-mismatch | Y.enterocolitica cgMLST | Single-linkage | 5 | experimental | 175 (254 isolates) |
| Y.enterocolitica_3-mismatch | Y.enterocolitica cgMLST | Single-linkage | 3 | experimental | 5062 (51 isolates) |
| Y.enterocolitica_5-mismatch | Y.enterocolitica cgMLST | Single-linkage | 5 | experimental | 175 (254 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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