Full information on isolate LEPTOCUBA07 (id:959)
Provenance/primary metadata
- id
- 959
- isolate
- LEPTOCUBA07
- aliases
- 201900815; H-247.11
- clade
- P1
- species
- interrogans
- serogroup
- Canicola
- serovar
- Canicola
- isolation year
- 2011
- sequencing year
- 2019
- world region
- Caribbean
- country
- Cuba
- host
- human
- sample type
- Blood
- source lab
- IPK_leptospira
- comments
- 201900815
- sender
- Jean-François Mariet, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 22 updates show details
- date entered
- 2019-05-17
- datestamp
- 2025-07-22
Sequence bin
- method
- Illumina
- contigs
- 257
- total length
- 4,632,053 bp
- max length
- 119,776 bp
- mean length
- 18,024 bp
- N50
- 35,748
- L50
- 43
- N90
- 11,684
- L90
- 125
- N95
- 6,641
- L95
- 152
- %GC
- 34.99
- Ns
- 0
- gaps
- 0
- loci tagged
- 608
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 | 544 | 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 | 28 (53 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 27 (14 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 32 (12 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 26 (25 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 25 (27 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 29 (27 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 25 (27 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 25 (14 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (44 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 27 (53 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 26 (53 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 28 (53 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 27 (14 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 32 (12 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 26 (25 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 25 (27 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 29 (27 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 25 (27 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 25 (14 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (44 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 27 (53 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 26 (53 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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