Full information on isolate IP38880 (id:2740)
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
- 2740
- isolate
- IP38880
- species phenotypic
- pseudotuberculosis
- serotype
- I
- species genotypic
- pseudotuberculosis
- genotype
- 2
- isolation date
- 16/04/2017
- category
- Clinical
- origin
- stool
- age
- 8
- sex
- M
- comments
- jusqu'au 12/05/2019 assignation: Y.pseudotuberculosis genotype 2
- sender
- Cyril Savin, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 11 updates show details
- date entered
- 2017-05-12
- datestamp
- 2019-10-29
- date received
- 2017-04-19
- CP labo
- 59016
- country code
- FRA
- country
- France
Sequence bin
- method
- Unknown
- contigs
- 93
- total length
- 4,408,007 bp
- max length
- 253,057 bp
- mean length
- 47,398 bp
- N50
- 145,503
- L50
- 11
- N90
- 34,193
- L90
- 38
- N95
- 27,829
- L95
- 45
- %GC
- 47.76
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,925
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 | 460 | 92 | |
| Y.enterocolitica cgMLST | 1727 | 460 | 26 | |
| Y.pseudotuberculosis cgMLST | 1921 | 1818 | 94 | |
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
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