Full information on isolate LO-3 (id:248)
Provenance/primary metadata
- id
- 248
- isolate
- LO-3
- biosample
- SAMN03783263
- accession number
- 211880
- clade
- P1
- species
- interrogans
- serogroup
- Canicola
- serovar
- Canicola
- sequencing year
- 2015
- world region
- South America
- country
- Brazil
- host
- Pig
- sample type
- Liver
- source lab
- Craig Venter Institute
- sender
- Julien Guglielmini, Institut Pasteur
- curator
- Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
- update history
- 773 updates show details
- date entered
- 2016-12-01
- datestamp
- 2022-12-07
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
- Unknown
- contigs
- 181
- total length
- 4,718,517 bp
- max length
- 194,239 bp
- mean length
- 26,070 bp
- N50
- 49,857
- L50
- 33
- N90
- 14,797
- L90
- 102
- N95
- 7,816
- L95
- 124
- %GC
- 35.04
- Ns
- 12
- gaps
- 11
- 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 | 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 | 28 (53 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 27 (14 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 32 (12 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 26 (25 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 25 (27 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 29 (27 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 25 (27 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 25 (14 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (44 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 27 (53 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 26 (53 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 28 (53 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 27 (14 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 32 (12 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 26 (25 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 25 (27 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 29 (27 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 25 (27 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 25 (14 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 5 (44 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 27 (53 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 26 (53 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Analysis: