Full information on isolate 2020/00246 (id:9342)
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
- 9342
- isolate
- 2020/00246
- alias
- IP43377
- species genotypic
- pseudotuberculosis
- genotype
- 2
- isolation date
- 21/02/2020
- sender
- Rémi Beau, Institut Pasteur, Paris
- curator
- Cyril Savin, Institut Pasteur, Paris (E-mail: cyril.savin@pasteur.fr)
- update history
- 8 updates show details
- date entered
- 2020-03-02
- datestamp
- 2020-03-02
Sequence bin
- method
- Illumina
- contigs
- 228
- total length
- 4,708,399 bp
- max length
- 134,554 bp
- mean length
- 20,651 bp
- N50
- 42,050
- L50
- 34
- N90
- 11,925
- L90
- 115
- N95
- 7,068
- L95
- 139
- %GC
- 47.69
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,020
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 | 1920 | 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 | 83 (21 isolates) |
| Y.pseudotuberculosis_5-mismatch | Y.pseudotuberculosis cgMLST | Single-linkage | 5 | experimental | 83 (21 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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