Full information on isolate 1548 (id:1508)
Provenance/primary metadata
- id
- 1508
- isolate
- 1548
- biosample
- SAMN12721655
- accession number
- GCF_014858935.1
- clade
- P1
- species
- interrogans
- serogroup
- Unknown
- serovar
- Bataviae
- isolation year
- 2015
- sequencing year
- 2019
- world region
- South-eastern Asia
- country
- Malaysia
- city
- Klang
- host
- human
- sample type
- Culture
- source lab
- Genbank
- sender
- Vallier SORDOILLET, CNR Leptospirose PASTEUR
- curator
- Jean-François Mariet, Institut Pasteur, Paris, France (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 9 updates show details
- date entered
- 2023-01-27
- datestamp
- 2025-12-09
Sequence bin
- method
- other
- contigs
- 4
- total length
- 4,880,112 bp
- max length
- 4,354,848 bp
- mean length
- 1,220,028 bp
- N50
- 4,354,848
- L50
- 1
- N90
- 393,564
- L90
- 2
- N95
- 393,564
- L95
- 2
- %GC
- 35.16
- Ns
- 0
- gaps
- 0
- loci tagged
- 548
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 | 545 | 100 | |
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 | 4 (15 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 4 (15 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 4 (10 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 4 (11 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 4 (11 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 4 (11 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 4 (15 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 4 (11 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 4 (15 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 4 (15 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 4 (15 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 4 (15 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 4 (10 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 4 (11 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 4 (11 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 4 (11 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 4 (15 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 4 (11 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 4 (15 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 4 (15 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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