Full information on isolate 75865 (id:4804)
Provenance/primary metadata
- id
- 4804
- isolate
- 75865
- species
- C. diphtheriae
- tox gene PCR
- Positive
- isolation year
- 2023
- country
- South Africa
- continent
- Africa
- state or locality
- Western Cape
- travel history
- Unknown
- host
- Human
- source
- Throat
- infection or disease
- asymptomatic carrier
- sender
- Rito Mikhari, National Institute for Communicable Diseases, South Africa, South Africa
- curator
- Virginie Passet, Institut Pasteur, France (E-mail: virginie.passet@pasteur.fr)
- update history
- 5 updates show details
- date entered
- 2024-02-06
- datestamp
- 2024-03-26
- outbreak or sporadic
- Cluster
Sequence bin
- method
- Illumina
- contigs
- 41
- total length
- 2,448,328 bp
- max length
- 195,503 bp
- mean length
- 59,716 bp
- N50
- 135,579
- L50
- 8
- N90
- 40,005
- L90
- 20
- N95
- 27,375
- L95
- 23
- %GC
- 53.53
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,312
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_239_0_0_0_0_1_0_0
- Species
- C. diphtheriae
- Lineage
- 0_0
- Sublineage
- SL906
- Clonal group
- ClG906
- Genetic cluster
- GC35
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 |
|---|---|---|---|---|---|
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 394 (12 isolates) |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 1022 (12 isolates) |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 394 (12 isolates) |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 1022 (12 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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