Full information on isolate 2018/00514 (id:4129)
Provenance/primary metadata
- id
- 4129
- isolate
- 2018/00514
- alias
- IP40258
- species genotypic
- pseudotuberculosis
- genotype
- 16
- isolation date
- 26/04/2018
- category
- Clinical
- origin
- blood
- age
- 51
- sex
- M
- comments
- jusqu'au 12/05/2019 assignation: Y.pseudotuberculosis genotype 16
- sender
- Sylvie Brémont, Institut Pasteur, Paris
- curator
- Cyril Savin, Institut Pasteur, Paris (E-mail: cyril.savin@pasteur.fr)
- update history
- 16 updates show details
- date entered
- 2018-05-14
- datestamp
- 2019-05-13
- date received
- 2018-05-02
- CP patient
- 54300
- CP labo
- 54300
- country code
- FRA
- country
- France
Sequence bin
- method
- Unknown
- contigs
- 86
- total length
- 4,611,032 bp
- max length
- 498,390 bp
- mean length
- 53,617 bp
- N50
- 141,291
- L50
- 10
- N90
- 48,923
- L90
- 30
- N95
- 36,764
- L95
- 35
- %GC
- 47.47
- Ns
- 34
- gaps
- 4
- loci tagged
- 1,997
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 | 500 | 28 | |
| Y.pseudotuberculosis cgMLST | 1921 | 1919 | 99 | |
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.pseudotuberculosis_5-mismatch | Y.pseudotuberculosis cgMLST | Single-linkage | 5 | experimental | 307 (2 isolates) |
| Y.pseudotuberculosis_5-mismatch | Y.pseudotuberculosis cgMLST | Single-linkage | 5 | experimental | 307 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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