Full information on isolate 9ca47288 (id:3497)
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
- 3497
- isolate
- 9ca47288
- species
- C. diphtheriae
- isolation year
- 2022
- country
- Switzerland
- continent
- Europe
- state or locality
- St Gallen
- travel history
- unknown
- host
- human
- infection or disease
- pharyngeal swab
- accession number
- ERS14359422
- sender
- Helena Seth-Smith, University of Zurich
- curator
- Auto Tagger
- update history
- 3 updates show details
- embargo history
- show details
- date entered
- 2022-12-16
- datestamp
- 2023-02-04
Sequence bin
- method
- Illumina
- contigs
- 41
- total length
- 2,606,230 bp
- max length
- 470,982 bp
- mean length
- 63,567 bp
- N50
- 402,423
- L50
- 3
- N90
- 45,345
- L90
- 14
- N95
- 23,098
- L95
- 18
- %GC
- 52.62
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,362
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
Analysis
rMLST species identification
Analysis performed: 2024-12-12
Similar isolates (determined by LIN codes)
- Scheme
- cgMLST
- LIN code
- 0_0_21_0_4_0_0_0_0_0
- Species
- C. diphtheriae
- Lineage
- 0_0
- Sublineage
- SL377
- Clonal group
- ClG377
- Genetic cluster
- GC2
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 | 38 (183 isolates) | SL: 377 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 817 (142 isolates) | |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 38 (183 isolates) | SL: 377 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 817 (142 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Analysis: