Full information on isolate 20221107_DIFT220 (id:5929)
Provenance/primary metadata
- id
- 5929
- isolate
- 20221107_DIFT220
- alias
- DIFT220
- species
- C. diphtheriae
- biovar
- Mitis
- tox gene PCR
- Positive
- tox production Elek
- Positive
- isolation year
- 2022
- city
- 2950
- country
- Belgium
- continent
- Europe
- state or locality
- Antwerp Province
- 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
- 15 updates show details
- embargo history
- show details
- date entered
- 2024-08-02
- datestamp
- 2026-07-09
Sequence bin
- method
- Illumina
- contigs
- 44
- total length
- 2,446,019 bp
- max length
- 471,240 bp
- mean length
- 55,592 bp
- N50
- 403,168
- L50
- 3
- N90
- 38,727
- L90
- 14
- N95
- 23,352
- L95
- 18
- %GC
- 53.55
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,319
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_21_0_4_0_0_0_1_0
- Species
- C. diphtheriae
- Lineage
- 0_0
- Sublineage
- SL377
- Clonal group
- ClG377
- Genetic cluster
- GC2
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_21_0_4_0 | 8 | 155 |
| 0_0_21_0_4_0_0 | 4 | 154 |
| 0_0_21_0_4_0_0_0 | 2 | 148 |
| 0_0_21_0_4_0_0_0_1 | 1 | 114 |
| 0_0_21_0_4_0_0_0_1_0 | 0 | 111 |
| 0 | 1220 | 2242 |
| 0_0 | 1035 | 2024 |
| 0_0_21 | 500 | 200 |
| 0_0_21_0 | 55 | 183 |
| 0_0_21_0_4 | 25 | 155 |
| 0_0_21_0_4_0 | 8 | 155 |
| 0_0_21_0_4_0_0 | 4 | 154 |
| 0_0_21_0_4_0_0_0 | 2 | 148 |
| 0_0_21_0_4_0_0_0_1 | 1 | 114 |
| 0_0_21_0_4_0_0_0_1_0 | 0 | 111 |
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
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