Full information on isolate 202101028 (id:1173)
Provenance/primary metadata
- id
- 1173
- isolate
- 202101028
- alias
- pomona_nenad
- clade
- P1
- species
- kirschneri
- serogroup
- Not examined
- serovar
- Not examined
- sequencing year
- 2021
- world region
- Eastern Europe
- country
- Croatia
- host
- unknown
- sample type
- Culture
- source lab
- CNR_leptospirose
- sender
- Jean-François Mariet
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 12 updates show details
- date entered
- 2021-07-05
- datestamp
- 2024-04-17
Sequence bin
- method
- Illumina
- contigs
- 505
- total length
- 4,845,177 bp
- max length
- 107,243 bp
- mean length
- 9,595 bp
- N50
- 22,225
- L50
- 64
- N90
- 5,893
- L90
- 219
- N95
- 3,526
- L95
- 272
- %GC
- 35.84
- Ns
- 0
- gaps
- 0
- loci tagged
- 584
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (warn threshold: 500) | |
| Assembly size | ||
| Minimum N50 | ||
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| cgMLST | 545 | 524 | 96 | |
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
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