Full information on isolate 202000073 (id:1890)
Provenance/primary metadata
- id
- 1890
- isolate
- 202000073
- aliases
- C19; FMAS_PN1
- biosample
- SAMN11919590
- accession number
- ASM1840380v1
- clade
- P1
- species
- borgpetersenii
- serogroup
- Javanica
- serovar
- not examined
- sequencing year
- 2021
- passage
- >10
- world region
- Southern Asia
- country
- Sri Lanka
- city
- Polonnaruwa
- host
- human
- sample type
- Blood
- source lab
- FMAS-Leptospira research lab
- age yr
- 56
- sex
- male
- sender
- Jean-François Mariet
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 20 updates show details
- date entered
- 2024-10-03
- datestamp
- 2025-04-17
Versions
More than one version of this isolate record exist.
- Older versions
- 1024
Sequence bin
- method
- Unknown
- contigs
- 2
- total length
- 3,917,612 bp
- max length
- 3,596,207 bp
- mean length
- 1,958,806 bp
- N50
- 3,596,207
- L50
- 1
- N90
- 3,596,207
- L90
- 1
- N95
- 321,405
- L95
- 2
- %GC
- 40.09
- Ns
- 0
- gaps
- 0
- loci tagged
- 620
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 | 267 (38 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 24 (39 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 273 (8 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-50 | cgMLST | Single-linkage | 50 | experimental | 24 (39 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 273 (8 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
Tools
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