Full information on isolate 20221202_DIFT235 (id:5942)
Provenance/primary metadata
- id
- 5942
- isolate
- 20221202_DIFT235
- alias
- DIFT235
- species
- C. diphtheriae
- biovar
- Mitis
- tox gene PCR
- Positive
- tox production Elek
- Positive
- isolation year
- 2022
- city
- 1831
- country
- Belgium
- continent
- Europe
- state or locality
- Flemish Brabant
- travel history
- Afghanistan
- host
- Human
- source
- Skin lesion
- infection or disease
- Skin lesion
- comments
- Refugee
- epidemic cluster
- J
- sender
- Helena Martini
- curator
- Helena Martini, Laboratorium Microbiologie, Universitair Ziekenhuis Brussel, Belgium (E-mail: Helena.Martini@uzbrussel.be)
- update history
- 17 updates show details
- embargo history
- show details
- date entered
- 2024-08-02
- datestamp
- 2026-07-09
Sequence bin
- method
- Illumina
- contigs
- 78
- total length
- 2,469,498 bp
- max length
- 175,971 bp
- mean length
- 31,661 bp
- N50
- 65,610
- L50
- 13
- N90
- 23,382
- L90
- 38
- N95
- 15,135
- L95
- 45
- %GC
- 53.59
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,309
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
- Species
- C. diphtheriae
- Lineage
- 0_0
- Sublineage
- SL574
- Clonal group
- ClG574
- Genetic cluster
- GC1
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_85_1_0_0 | 8 | 182 |
| 0_0_85_1_0_0_0 | 4 | 181 |
| 0_0_85_1_0_0_0_0 | 2 | 130 |
| 0_0_85_1_0_0_0_0_0 | 1 | 113 |
| 0_0_85_1_0_0_0_0_0_0 | 0 | 112 |
| 0 | 1220 | 2242 |
| 0_0 | 1035 | 2024 |
| 0_0_85 | 500 | 194 |
| 0_0_85_1 | 55 | 182 |
| 0_0_85_1_0 | 25 | 182 |
| 0_0_85_1_0_0 | 8 | 182 |
| 0_0_85_1_0_0_0 | 4 | 181 |
| 0_0_85_1_0_0_0_0 | 2 | 130 |
| 0_0_85_1_0_0_0_0_0 | 1 | 113 |
| 0_0_85_1_0_0_0_0_0_0 | 0 | 112 |
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 (186 isolates) | SL: 698 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 795 (170 isolates) | |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 293 (186 isolates) | SL: 698 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 795 (170 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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