Full information on isolate D5476 (id:1818)
Provenance/primary metadata
- id
- 1818
- isolate
- D5476
- alias
- SRR1993471
- country
- USA
- continent
- North America
- region
- Kansas
- year
- 1998
- disease
- gastroenteritis
- source
- human stool
- epidemiology
- general outbreak
- species
- Campylobacter jejuni
- penner
- 19
- ENA run accession
- SRR1993471 www.ebi.ac.uk
- sender
- Andrew Sails, CDC, Atlanta, USA
- curator
- Auto Tagger
- update history
- 34 updates show details
- date entered
- 2002-07-15
- datestamp
- 2022-08-25
Publication (1)
- Fitzgerald C, Helsel LO, Nicholson MA, Olsen SJ, Swerdlow DL, Flahart R, Sexton J, Fields PI (2001). Evaluation of methods for subtyping Campylobacter jejuni during an outbreak involving a food handler. J Clin Microbiol 39:2386-90
Sequence bin
- contigs
- 35
- total length
- 1,649,847 bp
- max length
- 196,730 bp
- mean length
- 47,139 bp
- N50
- 147,050
- L50
- 5
- N90
- 45,928
- L90
- 13
- N95
- 22,233
- L95
- 15
- %GC
- 30.48
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,549
Annotation quality metrics
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| MLST | 7 | 7 | 100 | |
| Ribosomal MLST | 53 | 53 | 100 | |
| C. jejuni / C. coli cgMLST v1.0 | 1343 | 1329 | 98 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Campylobacter jejuni | Pseudomonadota > Epsilonproteobacteria > Campylobacterales > Campylobacteraceae > Campylobacter > Campylobacter jejuni | 100% |
Analysis performed: 2023-02-05
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 |
|---|---|---|---|---|---|
| Cjc_cgc_200 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 200 | experimental | 8 (365 isolates) |
| Cjc_cgc_100 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 100 | experimental | 9 (238 isolates) |
| Cjc_cgc_50 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 50 | experimental | 10 (4 isolates) |
| Cjc_cgc_25 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 25 | experimental | 11 (4 isolates) |
| Cjc_cgc_10 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 10 | experimental | 12 (4 isolates) |
| Cjc_cgc_5 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 5 | experimental | 12 (4 isolates) |
| Cjc_cgc_200 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 200 | experimental | 8 (365 isolates) |
| Cjc_cgc_100 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 100 | experimental | 9 (238 isolates) |
| Cjc_cgc_50 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 50 | experimental | 10 (4 isolates) |
| Cjc_cgc_25 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 25 | experimental | 11 (4 isolates) |
| Cjc_cgc_10 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 10 | experimental | 12 (4 isolates) |
| Cjc_cgc_5 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 5 | experimental | 12 (4 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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