Full information on isolate 201702696 (id:584)
Provenance/primary metadata
- id
- 584
- isolate
- 201702696
- alias
- 2(1)
- biosample
- SAMEA5168321
- 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
- Zinini Farida, Institut Pasteur, Paris
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 24 updates show details
- date entered
- 2017-11-27
- datestamp
- 2024-04-17
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
- contigs
- 133
- total length
- 3,876,392 bp
- max length
- 346,470 bp
- mean length
- 29,146 bp
- N50
- 79,476
- L50
- 13
- N90
- 26,445
- L90
- 43
- N95
- 11,781
- L95
- 54
- %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 | 542 | 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 (11 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 22 (11 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 26 (4 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 22 (11 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 25 (30 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (146 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 (11 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 22 (11 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 26 (4 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 22 (11 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 25 (30 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (146 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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