Full information on isolate 201900828 (id:967)
Provenance/primary metadata
- id
- 967
- isolate
- 201900828
- aliases
- H-760.11; LEPTOCUBA20
- clade
- P1
- species
- kirschneri
- serogroup
- Pomona
- serovar
- Mozdok
- isolation year
- 2011
- world region
- Caribbean
- country
- Cuba
- host
- human
- sample type
- Blood
- source lab
- IPK_leptospira
- comments
- pathogen
- sender
- Céline Lorioux, Institut Pasteur, Paris
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 20 updates show details
- date entered
- 2019-05-28
- datestamp
- 2024-04-17
Sequence bin
- method
- Illumina
- contigs
- 371
- total length
- 4,127,915 bp
- max length
- 59,637 bp
- mean length
- 11,127 bp
- N50
- 19,150
- L50
- 73
- N90
- 6,282
- L90
- 223
- N95
- 3,988
- L95
- 263
- %GC
- 36.24
- Ns
- 9
- gaps
- 1
- loci tagged
- 606
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | N50 too low (warn threshold: 20,000) | |
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| cgMLST | 545 | 535 | 98 | |
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 | 73 (22 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 70 (22 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 75 (22 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 70 (22 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 66 (22 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 73 (22 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 70 (22 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 75 (22 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 70 (22 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 66 (22 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Analysis: