Full information on isolate 201702695 (id:583)
Provenance/primary metadata
- id
- 583
- isolate
- 201702695
- alias
- 2(2)
- biosample
- SAMEA5168320
- clade
- P1
- species
- borgpetersenii
- serogroup
- Unknown
- serovar
- Unknown
- isolation year
- 2017
- passage
- P3
- world region
- South-eastern Asia
- country
- Malaysia
- city
- Kajang
- host
- rat
- sample type
- Unknown
- source lab
- Institute for Medical Research, Mal
- sender
- Farida Zinini, Institut Pasteur, Paris
- curator
- Auto Tagger
- update history
- 26 updates show details
- date entered
- 2017-11-27
- datestamp
- 2025-07-22
Publications (2)
- Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M (2019). Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Negl Trop Dis 13:e0007374
- Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M (2020). Correction: Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Negl Trop Dis 14:e0008673
Sequence bin
- method
- Illumina
- contigs
- 107
- total length
- 3,876,383 bp
- max length
- 346,572 bp
- mean length
- 36,228 bp
- N50
- 112,312
- L50
- 12
- N90
- 25,506
- L90
- 34
- N95
- 14,732
- L95
- 43
- %GC
- 40.08
- Ns
- 0
- gaps
- 0
- loci tagged
- 621
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 | 267 (38 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 24 (39 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 23 (8 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 22 (8 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 26 (4 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 22 (8 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 25 (30 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (135 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 24 (39 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 23 (39 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 267 (38 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 24 (39 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 23 (8 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 22 (8 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 26 (4 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 22 (8 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 25 (30 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (135 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 24 (39 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 23 (39 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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