Full information on isolate L0864 (id:59)
Provenance/primary metadata
- id
- 59
- isolate
- L0864
- biosample
- SAMN00739396
- accession number
- 1049765
- clade
- P1
- species
- borgpetersenii
- serogroup
- Javanica
- serovar
- Javanica
- sequencing year
- 2012
- world region
- South-eastern Asia
- country
- Thailand
- host
- human
- sample type
- Unknown
- source lab
- Craig Venter Institute
- sender
- Julien Guglielmini, Institut Pasteur, France
- curator
- Jean-François Mariet, Institut Pasteur, Paris, France (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 1061 updates show details
- date entered
- 2016-12-01
- 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
- method
- Unknown
- contigs
- 178
- total length
- 3,855,185 bp
- max length
- 135,962 bp
- mean length
- 21,659 bp
- N50
- 56,786
- L50
- 24
- N90
- 16,827
- L90
- 75
- N95
- 10,312
- L95
- 89
- %GC
- 40.06
- Ns
- 105
- gaps
- 18
- loci tagged
- 621
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 | 544 | 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 | 267 (38 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 24 (4 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 24 (39 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 42 (2 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 23 (8 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 22 (8 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 39 (3 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 22 (8 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 22 (4 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 22 (4 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 25 (30 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (135 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 24 (39 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 23 (39 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 267 (38 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 24 (4 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 24 (39 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 42 (2 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 23 (8 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 22 (8 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 39 (3 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 22 (8 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 22 (4 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 22 (4 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 25 (30 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (135 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 24 (39 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 23 (39 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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