Full information on isolate YEM0008 (id:362)
Projects
This isolate is a member of the following project:
- yemen2019
- Yemen 2017-2020 outbreak
Provenance/primary metadata
- id
- 362
- isolate
- YEM0008
- alias
- YE-NCPHL-513
- species
- C. diphtheriae
- biovar
- Gravis
- tox gene PCR
- Positive
- tox production Elek
- Positive
- isolation year
- 2018
- city
- Sanaa
- country
- Yemen
- continent
- Asia
- travel history
- Not documented
- host
- Human
- accession number
- ERR4332856
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 13 updates show details
- date entered
- 2019-08-30
- datestamp
- 2022-08-09
Publication (1)
- Badell E, Alharazi A, Criscuolo A, Almoayed KAA, Lefrancq N, Bouchez V, Guglielmini J, Hennart M, Carmi-Leroy A, Zidane N, Pascal-Perrigault M, Lebreton M, Martini H, Salje H, Toubiana J, Dureab F, Dhabaan G, Brisse S (2021). Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study. Lancet Microbe 2:e386-e396
Sequence bin
- contigs
- 41
- total length
- 2,401,485 bp
- max length
- 307,125 bp
- mean length
- 58,573 bp
- N50
- 160,689
- L50
- 5
- N90
- 39,106
- L90
- 17
- N95
- 26,342
- L95
- 21
- %GC
- 53.43
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,308
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
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 | 131 (107 isolates) | SL: 384 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 217 (105 isolates) | |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 131 (107 isolates) | SL: 384 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 217 (105 isolates) |
Schemes and loci
Tools
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