Full information on isolate UK02 (id:4007)
Projects
This isolate is a member of the following project:
- 2022_EuropeanWideReemergence_collection
- Collection of the Hoefer et al. study on a large-scale Corynebacterium diphtheriae outbreak among migrant populations in Europe in 2022
Provenance/primary metadata
- id
- 4007
- isolate
- UK02
- species
- C. diphtheriae
- tox gene PCR
- Positive
- tox production Elek
- Positive
- isolation year
- 2022
- city
- Eastbourne
- country
- UK
- continent
- Europe
- travel history
- TR,EL,RS,AL,XK,AT,DE,FR
- host
- Human
- source
- SKINSWAB
- infection or disease
- CUTA
- sender
- Josh D'Aeth
- curator
- Josh D'Aeth, UKHSA (E-mail: joshua.daeth@ukhsa.gov.uk)
- update history
- 6 updates show details
- date entered
- 2023-03-15
- datestamp
- 2024-07-24
Sequence bin
- contigs
- 69
- total length
- 2,466,968 bp
- max length
- 378,969 bp
- mean length
- 35,754 bp
- N50
- 100,018
- L50
- 7
- N90
- 19,698
- L90
- 25
- N95
- 15,129
- L95
- 32
- %GC
- 53.59
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,352
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
Similar isolates (determined by LIN codes)
- Scheme
- cgMLST
- LIN code
- 0_0_85_1_0_0_0_0_0_0
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 |
|---|---|---|---|---|---|---|
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 293 (151 isolates) | SL: 698 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 795 (139 isolates) | |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 293 (151 isolates) | SL: 698 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 795 (139 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Analysis: