Full information on isolate 5399 (id:102)
Provenance/primary metadata
- id
- 102
- isolate
- 5399
- biosample
- SAMN02436587
- accession number
- GCF_000243715.2
- clade
- P2
- species
- broomii
- serogroup
- Unknown
- serovar
- Unknown
- sequencing year
- 2012
- world region
- Western Europe
- country
- Denmark
- host
- human
- sample type
- Blood
- 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
- 1022 updates show details
- date entered
- 2016-12-01
- datestamp
- 2024-05-24
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
- 10
- total length
- 4,485,045 bp
- max length
- 3,575,710 bp
- mean length
- 448,505 bp
- N50
- 3,575,710
- L50
- 1
- N90
- 145,065
- L90
- 3
- N95
- 139,056
- L95
- 4
- %GC
- 42.93
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,118
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 | 523 | 95 | |
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 | 60 (2 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 59 (2 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 62 (2 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 59 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 56 (2 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 60 (2 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 57 (1 isolate) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 59 (2 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 69 (1 isolate) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 56 (1 isolate) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 55 (1 isolate) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 65 (1 isolate) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 54 (1 isolate) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 53 (1 isolate) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 52 (1 isolate) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 62 (2 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 49 (1 isolate) |
| test40_capture_cgMLST | capture_cgMLST | Single-linkage | 40 | experimental | 17 (1 isolate) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 59 (2 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 56 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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