Full information on isolate IP1610023 (id:472)
Provenance/primary metadata
- id
- 472
- isolate
- IP1610023
- biosample
- SAMEA5168226
- clade
- P1
- species
- interrogans
- serogroup
- Pomona
- serovar
- Unknown
- world region
- South America
- country
- Uruguay
- host
- bovine
- sample type
- Unknown
- source lab
- IP Montevideo
- sender
- Farida Zinini, Institut Pasteur, Paris
- curator
- Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
- update history
- 23 updates show details
- date entered
- 2017-04-24
- 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
- 540
- total length
- 4,023,824 bp
- max length
- 62,159 bp
- mean length
- 7,452 bp
- N50
- 11,063
- L50
- 110
- N90
- 3,665
- L90
- 353
- N95
- 2,687
- L95
- 415
- %GC
- 35.64
- Ns
- 8
- gaps
- 1
- loci tagged
- 614
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (warn threshold: 500) | |
| Assembly size | ||
| Minimum N50 | N50 too low (warn threshold: 20,000) | |
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| cgMLST | 545 | 538 | 98 | |
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 | 5 (74 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 5 (30 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 5 (74 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 118 (23 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 5 (39 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 5 (39 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 5 (39 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 5 (41 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 5 (30 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (44 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 5 (73 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 5 (74 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 5 (74 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 5 (74 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 5 (30 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 5 (74 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 118 (23 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 5 (39 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 5 (39 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 5 (39 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 5 (41 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 5 (30 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (44 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 5 (73 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 5 (74 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 5 (74 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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