Full information on isolate L.santarosai Rr5 (id:1535)
Provenance/primary metadata
- id
- 1535
- isolate
- L.santarosai Rr5
- alias
- Rr5
- biosample
- SAMN34670628
- species
- santarosai
- serogroup
- Unknown
- serovar
- Unknown
- isolation year
- 1973
- sequencing year
- 2023
- world region
- South America
- country
- Brazil
- host
- rat
- sample type
- Unknown
- source lab
- Genbank
- sender
- Vallier SORDOILLET, CNR Leptospirose PASTEUR
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 4 updates show details
- date entered
- 2023-07-11
- datestamp
- 2024-07-15
Sequence bin
- contigs
- 179
- total length
- 4,050,492 bp
- max length
- 226,414 bp
- mean length
- 22,629 bp
- N50
- 70,190
- L50
- 18
- N90
- 17,223
- L90
- 66
- N95
- 7,260
- L95
- 85
- %GC
- 41.88
- Ns
- 0
- gaps
- 0
- loci tagged
- 546
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| cgMLST | 545 | 536 | 98 | |
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 |
|---|---|---|---|---|---|
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 427 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 417 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 438 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 414 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 402 (2 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 427 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 417 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 438 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 414 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 402 (2 isolates) |
Schemes and loci
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