Full information on isolate NIH08001 (id:221)
Provenance/primary metadata
- id
- 221
- isolate
- NIH08001
- isolation year
- 2008
- world region
- North America
- country
- USA
- host
- Human
- other strain info
- ST5 ; CC2 ; group A
- source
- Blood
- infection
- Infection
- other infection info
- Disease
- MSSE MRSE
- MRSE
- sender
- Julien Guglielmini, Institut Pasteur
- curator
- Auto Tagger
- update history
- 8 updates show details
- date entered
- 2016-05-23
- datestamp
- 2022-12-22
Publication (1)
- Conlan S, Mijares LA, Becker J, Blakesley RW, Bouffard GG, Brooks S, Coleman H, Gupta J, Gurson N, Park M, Schmidt B, Thomas PJ, Otto M, Kong HH, Murray PR, Segre JA (2012). Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates. Genome Biol 13:R64
Sequence bin
- contigs
- 68
- total length
- 2,509,449 bp
- max length
- 328,303 bp
- mean length
- 36,904 bp
- N50
- 88,613
- L50
- 9
- N90
- 30,766
- L90
- 26
- N95
- 19,703
- L95
- 31
- %GC
- 32.14
- Ns
- 0
- gaps
- 0
- loci tagged
- 767
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 | 6 (41 isolates) |
| Clustering-468 | cgMLST | Single-linkage | 468 | experimental | 1 (417 isolates) |
| test-105 | cgMLST | Single-linkage | 105 | experimental | 6 (41 isolates) |
| Clustering-134 | cgMLST | Single-linkage | 134 | experimental | 6 (41 isolates) |
| Clustering-468 | cgMLST | Single-linkage | 468 | experimental | 1 (417 isolates) |
| test-105 | cgMLST | Single-linkage | 105 | experimental | 6 (41 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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