Full information on isolate FRC0050_P2M-2024 (id:5255)
Projects
This isolate is a member of the following project:
- Corynebacterium_Nanopore_R10_2025
- Benchmarking Nanopore R10 sequencing vs Illumina for cgMLST typing
Provenance/primary metadata
- id
- 5255
- isolate
- FRC0050_P2M-2024
- species
- C. diphtheriae
- biovar
- Mitis
- tox gene PCR
- Positive
- tox production Elek
- Positive
- isolation year
- 2009
- country
- Mayotte
- continent
- Africa
- state or locality
- Mayotte
- travel history
- Not documented
- host
- Human
- source
- Respiratory
- infection or disease
- Upper RTI
- other source info
- Pharyngeal
- sender
- Virginie Passet, Institut Pasteur, France
- curator
- Sylvain Brisse, Institut Pasteur, Paris, France (E-mail: sylvain.brisse@pasteur.fr)
- update history
- 4 updates show details
- embargo history
- show details
- date entered
- 2024-02-27
- datestamp
- 2025-04-30
Sequence bin
- method
- Unknown
- contigs
- 39
- total length
- 2,428,505 bp
- max length
- 539,701 bp
- mean length
- 62,270 bp
- N50
- 229,352
- L50
- 4
- N90
- 35,192
- L90
- 17
- N95
- 29,406
- L95
- 21
- %GC
- 53.48
- Ns
- 44
- gaps
- 35
- loci tagged
- 1,304
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_128_2_0_0_0_0_1_0
- Species
- C. diphtheriae
- Lineage
- 0_0
- Sublineage
- SL490
- Clonal group
- ClG184
- Genetic cluster
- GC5
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_128_2_0_0 | 8 | 51 |
| 0_0_128_2_0_0_0 | 4 | 51 |
| 0_0_128_2_0_0_0_0 | 2 | 51 |
| 0_0_128_2_0_0_0_0_1 | 1 | 49 |
| 0_0_128_2_0_0_0_0_1_0 | 0 | 49 |
| 0 | 1220 | 2380 |
| 0_0 | 1035 | 2162 |
| 0_0_128 | 500 | 56 |
| 0_0_128_2 | 55 | 51 |
| 0_0_128_2_0 | 25 | 51 |
| 0_0_128_2_0_0 | 8 | 51 |
| 0_0_128_2_0_0_0 | 4 | 51 |
| 0_0_128_2_0_0_0_0 | 2 | 51 |
| 0_0_128_2_0_0_0_0_1 | 1 | 49 |
| 0_0_128_2_0_0_0_0_1_0 | 0 | 49 |
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 | 65 (56 isolates) | SL: 184 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 86 (51 isolates) | |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 65 (56 isolates) | SL: 184 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 86 (51 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: