Full information on isolate 201700037 (id:410)
Provenance/primary metadata
- id
- 410
- isolate
- 201700037
- biosample
- SAMEA5168186
- clade
- P1
- species
- kirschneri
- serogroup
- Canicola
- serovar
- Galtoni
- isolation year
- 1988
- sequencing year
- 2017
- world region
- South America
- country
- Argentina
- host
- bovine
- sample type
- Unknown
- source lab
- CNR_leptospirose
- sender
- Olivier Schiettekatte, Institut Pasteur
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 74 updates show details
- date entered
- 2017-02-13
- 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
- 244
- total length
- 4,318,566 bp
- max length
- 96,717 bp
- mean length
- 17,700 bp
- N50
- 33,248
- L50
- 42
- N90
- 10,498
- L90
- 130
- N95
- 6,982
- L95
- 154
- %GC
- 36.11
- Ns
- 9
- gaps
- 1
- loci tagged
- 1,156
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 | 537 | 98 | |
Similar isolates (determined by classification schemes)
Some groups only contain this isolate. Show single groups
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 | 129 (2 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 119 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 124 (2 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 115 (2 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 114 (2 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 111 (2 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 110 (2 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 106 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 135 (2 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 98 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 123 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 117 (2 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 129 (2 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 119 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 124 (2 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 206 (1 isolate) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 115 (2 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 114 (2 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 185 (1 isolate) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 111 (2 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 110 (2 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 106 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 135 (2 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 98 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 123 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 117 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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