Full information on isolate ERR10841009 (id:4446)
Projects
This isolate is a member of the following project:
- Diphtheria in Australia, 2017-2022
- Graham et al. 2023 (https://pubmed.ncbi.nlm.nih.gov/37212056/)
Provenance/primary metadata
- id
- 4446
- isolate
- ERR10841009
- alias
- M1709293
- species
- C. diphtheriae
- isolation year
- 2017
- country
- Australia
- continent
- Oceania
- travel history
- Not documented
- host
- Human
- accession number
- PRJEB58646
- sender
- Rikki Graham, Queensland Health Forensic and Scientific Services
- curator
- Auto Tagger
- update history
- 4 updates show details
- date entered
- 2023-05-30
- datestamp
- 2023-05-30
Publication (1)
- Graham RMA, Rathnayake IU, Sandhu S, Bhandari M, Taunton C, Fisher V, Hempenstall A, Marquardt T, Jennison AV (2023). Genomic analysis of an outbreak of toxin gene bearing Corynebacterium diphtheriae in Northern Queensland, Australia reveals high level of genetic similarity. Epidemiol Infect [Epub ahead of print]:1-17
Sequence bin
- method
- Illumina
- contigs
- 49
- total length
- 2,484,885 bp
- max length
- 469,401 bp
- mean length
- 50,712 bp
- N50
- 109,288
- L50
- 6
- N90
- 30,375
- L90
- 22
- N95
- 20,920
- L95
- 27
- %GC
- 53.60
- Ns
- 130
- gaps
- 4
- loci tagged
- 1,297
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_20_1_0_0_0_0_0_0
- Species
- C. diphtheriae
- Lineage
- 0_0
- Sublineage
- SL914
- Clonal group
- ClG10088
- Genetic cluster
- GC277
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 |
|---|---|---|---|---|---|
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 361 (4 isolates) |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 882 (2 isolates) |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 361 (4 isolates) |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 882 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Analysis: