Full information on isolate 201702693 (id:570)
Provenance/primary metadata
- id
- 570
- isolate
- 201702693
- alias
- 19(1)
- biosample
- SAMEA5168309
- clade
- P1
- species
- interrogans
- 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
- Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
- update history
- 25 updates show details
- date entered
- 2017-11-27
- datestamp
- 2023-02-02
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
- 189
- total length
- 4,558,561 bp
- max length
- 178,959 bp
- mean length
- 24,120 bp
- N50
- 59,622
- L50
- 24
- N90
- 20,466
- L90
- 74
- N95
- 10,549
- L95
- 88
- %GC
- 35.11
- Ns
- 0
- gaps
- 0
- loci tagged
- 603
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 | 531 | 97 | |
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 | 4 (15 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 4 (15 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 4 (10 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 4 (11 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 4 (11 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 4 (11 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 4 (15 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 4 (11 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 4 (15 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 4 (15 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 4 (15 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 4 (15 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 4 (10 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 4 (11 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 4 (11 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 4 (11 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 4 (15 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 4 (11 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 4 (15 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 4 (15 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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