Full information on isolate 201703071 (id:390)
Provenance/primary metadata
- id
- 390
- isolate
- 201703071
- alias
- 16(2)
- clade
- P1
- species
- interrogans
- serogroup
- Unknown
- serovar
- Unknown
- isolation year
- 2017
- passage
- P6
- world region
- South-eastern Asia
- country
- Malaysia
- city
- Kajang
- host
- rat
- source lab
- CNR_leptospirose
- comments
- DO <0,1 (0,082) culot sur 6ml
- sender
- Olivier Schiettekatte, Institut Pasteur
- curator
- Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
- update history
- 24 updates show details
- date entered
- 2018-02-02
- datestamp
- 2023-02-02
Sequence bin
- method
- Illumina
- contigs
- 331
- total length
- 4,591,894 bp
- max length
- 88,908 bp
- mean length
- 13,873 bp
- N50
- 28,474
- L50
- 51
- N90
- 8,273
- L90
- 169
- N95
- 4,629
- L95
- 204
- %GC
- 35.29
- Ns
- 475
- gaps
- 3
- loci tagged
- 619
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 | 540 | 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 | 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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