Full information on isolate 1280844 (id:1519)
Projects
This isolate is a member of the following project:
- cgMLST C. ulcerans set-up study
- Isolates included in the cgMLST study for C. ulcerans and C. ramonii (publicly-available genomes and some isolates from the French NRC)
Provenance/primary metadata
- id
- 1519
- isolate
- 1280844
- species
- C. ulcerans
- tox gene PCR
- Positive
- tox production Elek
- Positive
- isolation year
- 2021
- country
- UK [England]
- continent
- Europe
- travel history
- None
- host
- Dog
- source
- throat
- infection or disease
- carriage
- epidemic cluster
- Pet of: 1280830
- sender
- David Litt, UK Health Security Agency, UK [England]
- curator
- Chiara Crestani, Pasteur Institute, France (E-mail: chiara.crestani@pasteur.fr)
- update history
- 9 updates show details
- date entered
- 2022-01-20
- datestamp
- 2023-11-15
- outbreak or sporadic
- outbreak
Sequence bin
- method
- Illumina
- contigs
- 15
- total length
- 2,423,499 bp
- max length
- 793,255 bp
- mean length
- 161,567 bp
- N50
- 323,597
- L50
- 3
- N90
- 157,662
- L90
- 6
- N95
- 67,020
- L95
- 8
- %GC
- 53.36
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,619
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
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 | Fields |
|---|---|---|---|---|---|---|
| Clonal_group_ulcerans | cgMLST_ulcerans | Single-linkage | 194 | experimental | 46 (2 isolates) | CG: 787 |
| Genomic_cluster_ulcerans | cgMLST_ulcerans | Single-linkage | 25 | experimental | 327 (2 isolates) | |
| Sublineage_ulcerans | cgMLST_ulcerans | Single-linkage | 940 | experimental | 11 (19 isolates) | SL: 428 |
| Clonal_group_ulcerans | cgMLST_ulcerans | Single-linkage | 194 | experimental | 46 (2 isolates) | CG: 787 |
| Genomic_cluster_ulcerans | cgMLST_ulcerans | Single-linkage | 25 | experimental | 327 (2 isolates) | |
| Sublineage_ulcerans | cgMLST_ulcerans | Single-linkage | 940 | experimental | 11 (19 isolates) | SL: 428 |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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