Full information on isolate 1088_SEPI (id:56)
Provenance/primary metadata
- id
- 56
- isolate
- 1088_SEPI
- world region
- North America
- country
- USA
- host
- Human
- source
- Unknown
- infection
- Unknown
- sender
- Julien Guglielmini, Institut Pasteur
- curator
- Auto Tagger
- update history
- 7 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
- contigs
- 146
- total length
- 2,551,429 bp
- max length
- 208,189 bp
- mean length
- 17,476 bp
- N50
- 54,693
- L50
- 16
- N90
- 12,457
- L90
- 55
- N95
- 6,612
- L95
- 70
- %GC
- 31.94
- Ns
- 200
- gaps
- 2
- loci tagged
- 772
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 | 19 (141 isolates) |
| Clustering-468 | cgMLST | Single-linkage | 468 | experimental | 1 (417 isolates) |
| test-105 | cgMLST | Single-linkage | 105 | experimental | 19 (128 isolates) |
| Clustering-134 | cgMLST | Single-linkage | 134 | experimental | 19 (141 isolates) |
| Clustering-468 | cgMLST | Single-linkage | 468 | experimental | 1 (417 isolates) |
| test-105 | cgMLST | Single-linkage | 105 | experimental | 19 (128 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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