Full information on isolate 2020/00107 (id:9153)
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
- 9153
- isolate
- 2020/00107
- alias
- IP43237
- species genotypic
- pseudotuberculosis
- genotype
- 7
- isolation date
- 23/01/2020
- sender
- Sylvie Brémont, Institut Pasteur, Paris
- curator
- Auto Tagger
- update history
- 7 updates show details
- date entered
- 2020-02-03
- datestamp
- 2020-02-03
Sequence bin
- method
- Illumina
- contigs
- 193
- total length
- 4,670,621 bp
- max length
- 121,563 bp
- mean length
- 24,201 bp
- N50
- 43,837
- L50
- 35
- N90
- 15,480
- L90
- 101
- N95
- 8,763
- L95
- 120
- %GC
- 47.72
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,976
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 | 498 | 28 | |
| Y.pseudotuberculosis cgMLST | 1921 | 1911 | 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 | 116 (23 isolates) |
| Y.pseudotuberculosis_5-mismatch | Y.pseudotuberculosis cgMLST | Single-linkage | 5 | experimental | 116 (23 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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