Full information on isolate 109/90 (id:626)
Provenance/primary metadata
- id
- 626
- isolate
- 109/90
- clade
- P1
- species
- interrogans
- serogroup
- Icterohaemorrhagiae
- serovar
- Unknown
- passage
- P2
- world region
- Western Europe
- country
- France
- city
- Charleville
- host
- human
- source lab
- CNR_leptospirose
- sender
- Céline Lorioux, Institut Pasteur, Paris
- curator
- Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
- update history
- 21 updates show details
- date entered
- 2018-02-19
- datestamp
- 2023-02-02
Sequence bin
- method
- Illumina
- contigs
- 116
- total length
- 4,575,716 bp
- max length
- 227,764 bp
- mean length
- 39,446 bp
- N50
- 85,609
- L50
- 19
- N90
- 26,370
- L90
- 56
- N95
- 17,299
- L95
- 67
- %GC
- 35.00
- Ns
- 0
- gaps
- 0
- loci tagged
- 622
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 | 6 (146 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 6 (34 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 6 (146 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 58 (30 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 6 (36 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 6 (38 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 54 (36 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 6 (38 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 6 (34 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 6 (34 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 51 (145 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 6 (38 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 6 (146 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 6 (146 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 6 (146 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 6 (34 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 6 (146 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 58 (30 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 6 (36 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 6 (38 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 54 (36 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 6 (38 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 6 (34 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 6 (34 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 51 (145 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 6 (38 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 6 (146 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 6 (146 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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