Full information on isolate R6 (id:1493)
Provenance/primary metadata
- id
- 1493
- isolate
- R6
- alias
- R6L
- biosample
- SAMN11389084
- clade
- P1
- species
- borgpetersenii
- serogroup
- Unknown
- serovar
- Unknown
- isolation year
- 2017
- sequencing year
- 2019
- world region
- Caribbean
- country
- St. Kitts & Nevis
- host
- mouse
- 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
- 8 updates show details
- date entered
- 2023-01-27
- datestamp
- 2024-04-25
Sequence bin
- contigs
- 2
- total length
- 3,821,116 bp
- max length
- 3,513,910 bp
- mean length
- 1,910,558 bp
- N50
- 3,513,910
- L50
- 1
- N90
- 3,513,910
- L90
- 1
- N95
- 307,206
- L95
- 2
- %GC
- 39.98
- Ns
- 10200
- gaps
- 102
- loci tagged
- 520
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 | 518 | 95 | |
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 | 15 (118 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 15 (118 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 15 (118 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 15 (118 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 14 (118 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 15 (118 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 15 (118 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 15 (118 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 15 (118 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 14 (118 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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