Full information on isolate LEPTOCUBA04 (id:817)
Provenance/primary metadata
- id
- 817
- isolate
- LEPTOCUBA04
- aliases
- 201900813; H-192.12
- clade
- P1
- species
- borgpetersenii
- serogroup
- Ballum
- serovar
- Ballum
- isolation year
- 2012
- sequencing year
- 2019
- world region
- Caribbean
- country
- Cuba
- host
- human
- sample type
- Blood
- source lab
- IPK_leptospira
- comments
- 201900813
- sender
- Jean-François Mariet
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 20 updates show details
- date entered
- 2019-05-17
- datestamp
- 2024-04-17
Sequence bin
- contigs
- 119
- total length
- 3,904,502 bp
- max length
- 139,494 bp
- mean length
- 32,811 bp
- N50
- 62,425
- L50
- 22
- N90
- 20,957
- L90
- 65
- N95
- 15,898
- L95
- 76
- %GC
- 40.02
- Ns
- 0
- gaps
- 0
- loci tagged
- 609
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 | 543 | 99 | |
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
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