Full information on isolate TE 1992 (id:18)
Provenance/primary metadata
- id
- 18
- isolate
- TE 1992
- biosample
- SAMN01036683
- accession number
- 555588
- clade
- P1
- species
- interrogans
- serogroup
- Australis
- serovar
- Lora
- sequencing year
- 2012
- world region
- Middle Africa
- country
- Tanzania
- host
- other rodent
- sample type
- Unknown
- source lab
- Craig Venter Institute
- sender
- Julien Guglielmini, Institut Pasteur
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 886 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
- contigs
- 80
- total length
- 4,779,320 bp
- max length
- 287,993 bp
- mean length
- 59,742 bp
- N50
- 111,638
- L50
- 14
- N90
- 32,633
- L90
- 43
- N95
- 20,515
- L95
- 52
- %GC
- 35.06
- Ns
- 3
- gaps
- 3
- loci tagged
- 1,151
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 | 468 | 85 | |
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 |
|---|---|---|---|---|---|
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 12 (7 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 12 (16 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 11 (9 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 10 (9 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 10 (9 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 10 (7 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 10 (7 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 10 (9 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 57 (16 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 11 (16 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 12 (1 isolate) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 12 (7 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 12 (16 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 14 (1 isolate) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 11 (9 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 10 (9 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 13 (1 isolate) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 10 (9 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 10 (7 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 10 (7 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 12 (1 isolate) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 10 (9 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 57 (16 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 11 (16 isolates) |
Schemes and loci
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