Full information on isolate FRC1994 (id:4687)
Projects
This isolate is a member of the following project:
- 2023_EuropeanWideReemergence_followup
- EU isolates 2023 (Hoefer et al.)
Provenance/primary metadata
- id
- 4687
- isolate
- FRC1994
- species
- C. diphtheriae
- biovar
- Mitis
- tox gene PCR
- Positive
- tox production Elek
- Positive
- isolation year
- 2023
- country
- France
- continent
- Europe
- state or locality
- Mainland France
- travel history
- Afghanistan
- host
- Human
- source
- Cutaneous and soft tissue
- infection or disease
- Cutaneous and soft tissue infection
- other source info
- Superficial wound
- comments
- Originally from Afganistan
- accession number
- ERR13801626
- sender
- Virginie Passet, Institut Pasteur, France
- curator
- Auto Tagger
- update history
- 7 updates show details
- embargo history
- show details
- date entered
- 2023-10-06
- datestamp
- 2025-07-18
Sequence bin
- method
- Unknown
- contigs
- 42
- total length
- 2,471,831 bp
- max length
- 275,267 bp
- mean length
- 58,854 bp
- N50
- 143,959
- L50
- 6
- N90
- 33,578
- L90
- 18
- N95
- 19,745
- L95
- 23
- %GC
- 53.59
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,313
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 | 2380 |
| 0_0 | 1035 | 2162 |
| 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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