Full information on isolate D0445 (id:1820)
Provenance/primary metadata
- id
- 1820
- isolate
- D0445
- alias
- SRR1993342
- country
- USA
- continent
- North America
- region
- Florida
- year
- 1983
- disease
- gastroenteritis
- source
- human stool
- epidemiology
- general outbreak
- species
- Campylobacter jejuni
- penner
- 19
- ENA run accession
- SRR1993342 www.ebi.ac.uk
- sender
- Andrew Sails, CDC, Atlanta, USA
- curator
- Auto Tagger
- update history
- 35 updates show details
- date entered
- 2002-07-15
- datestamp
- 2022-08-25
Publication (1)
- Sacks JJ, Lieb S, Baldy LM, Berta S, Patton CM, White MC, Bigler WJ, Witte JJ (1986). Epidemic campylobacteriosis associated with a community water supply. Am J Public Health 76:424-8
Sequence bin
- contigs
- 49
- total length
- 1,674,111 bp
- max length
- 154,939 bp
- mean length
- 34,166 bp
- N50
- 125,811
- L50
- 6
- N90
- 19,584
- L90
- 21
- N95
- 11,118
- L95
- 26
- %GC
- 30.45
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,553
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 | 1328 | 98 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Campylobacter jejuni | Proteobacteria > Epsilonproteobacteria > Campylobacterales > Campylobacteraceae > Campylobacter > Campylobacter jejuni | 100% |
Analysis performed: 2023-01-11
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 (337 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 | 11 (7 isolates) |
| Cjc_cgc_25 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 25 | experimental | 12 (5 isolates) |
| Cjc_cgc_10 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 10 | experimental | 13 (5 isolates) |
| Cjc_cgc_5 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 5 | experimental | 13 (5 isolates) |
| Cjc_cgc_200 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 200 | experimental | 8 (337 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 | 11 (7 isolates) |
| Cjc_cgc_25 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 25 | experimental | 12 (5 isolates) |
| Cjc_cgc_10 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 10 | experimental | 13 (5 isolates) |
| Cjc_cgc_5 | C. jejuni / C. coli cgMLST v1.0 | Single-linkage | 5 | experimental | 13 (5 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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