Full information on isolate 178_SEPI (id:95)
Provenance/primary metadata
- id
- 95
- isolate
- 178_SEPI
- world region
- North America
- country
- USA
- host
- Human
- source
- Unknown
- infection
- Unknown
- sender
- Julien Guglielmini, Institut Pasteur, France
- curator
- Auto Tagger
- update history
- 5 updates show details
- date entered
- 2016-05-23
- datestamp
- 2022-12-22
Publication (1)
- Roach DJ, Burton JN, Lee C, Stackhouse B, Butler-Wu SM, Cookson BT, Shendure J, Salipante SJ (2015). A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota. PLoS Genet 11:e1005413
Sequence bin
- method
- Unknown
- contigs
- 69
- total length
- 2,508,600 bp
- max length
- 264,092 bp
- mean length
- 36,357 bp
- N50
- 82,465
- L50
- 10
- N90
- 26,353
- L90
- 30
- N95
- 12,205
- L95
- 38
- %GC
- 32.17
- Ns
- 208
- gaps
- 4
- loci tagged
- 768
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 |
|---|---|---|---|---|---|
| Clustering-134 | cgMLST | Single-linkage | 134 | experimental | 14 (13 isolates) |
| Clustering-468 | cgMLST | Single-linkage | 468 | experimental | 1 (417 isolates) |
| test-105 | cgMLST | Single-linkage | 105 | experimental | 14 (13 isolates) |
| Clustering-134 | cgMLST | Single-linkage | 134 | experimental | 14 (13 isolates) |
| Clustering-468 | cgMLST | Single-linkage | 468 | experimental | 1 (417 isolates) |
| test-105 | cgMLST | Single-linkage | 105 | experimental | 14 (13 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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