Full information on isolate 45903 (id:1580)
Projects
This isolate is a member of the following project:
- Oxford
- Isolates from former Oxford database
Provenance/primary metadata
- id
- 1580
- isolate
- 45903
- species
- C. diphtheriae
- tox gene PCR
- Positive
- tox production Elek
- Positive
- isolation year
- 2015
- country
- South Africa
- continent
- Africa
- state or locality
- Kwazulu-Natal
- travel history
- unknown
- host
- Human
- source
- tonsil
- infection or disease
- respiratory diphtheria
- sender
- Mushal Ali, NICD, South Africa
- curator
- Virginie Passet, Institut Pasteur (E-mail: virginie.passet@pasteur.fr)
- update history
- 16 updates show details
- date entered
- 2022-02-07
- datestamp
- 2024-03-26
- outbreak or sporadic
- outbreak
Sequence bin
- contigs
- 51
- total length
- 2,445,961 bp
- max length
- 351,179 bp
- mean length
- 47,961 bp
- N50
- 157,367
- L50
- 6
- N90
- 40,060
- L90
- 16
- N95
- 26,636
- L95
- 20
- %GC
- 53.57
- Ns
- 922
- gaps
- 13
- loci tagged
- 1,311
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
Tools
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