Full information on isolate 74873 (id:4390)
Provenance/primary metadata
- id
- 4390
- isolate
- 74873
- species
- C. diphtheriae
- tox gene PCR
- Positive
- isolation year
- 2023
- country
- South Africa
- continent
- Africa
- state or locality
- Kwazulu-Natal
- travel history
- None
- host
- human
- infection or disease
- cutaneous diphtheria
- sender
- Rito Mikhari, National Institute for Communicable Diseases, South Africa
- curator
- Virginie Passet, Institut Pasteur (E-mail: virginie.passet@pasteur.fr)
- update history
- 5 updates show details
- date entered
- 2023-09-18
- datestamp
- 2024-03-26
Sequence bin
- contigs
- 45
- total length
- 2,381,626 bp
- max length
- 351,189 bp
- mean length
- 52,926 bp
- N50
- 118,801
- L50
- 6
- N90
- 37,956
- L90
- 18
- N95
- 25,024
- L95
- 22
- %GC
- 53.56
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,313
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 |
|---|---|---|---|---|---|---|
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 265 (29 isolates) | SL: 378 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 472 (29 isolates) | |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 265 (29 isolates) | SL: 378 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 472 (29 isolates) |
Schemes and loci
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