Full information on isolate STPET07 (id:838)
Provenance/primary metadata
- id
- 838
- isolate
- STPET07
- alias
- Norway Rat 20
- clade
- P1
- species
- interrogans
- serogroup
- Unknown
- serovar
- Unknown
- isolation year
- 1980
- passage
- 114
- world region
- Central Asia
- country
- Russia
- city
- Leningrad
- host
- norway Rat
- sample type
- Kidney
- source lab
- St-Petersburg Pasteur Institute
- resistance info
- Pathogen
- sender
- Jean-François Mariet, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 22 updates show details
- date entered
- 2019-02-08
- datestamp
- 2025-07-22
Sequence bin
- method
- Illumina
- contigs
- 164
- total length
- 4,530,176 bp
- max length
- 181,250 bp
- mean length
- 27,624 bp
- N50
- 61,234
- L50
- 26
- N90
- 17,895
- L90
- 79
- N95
- 10,485
- L95
- 96
- %GC
- 35.01
- Ns
- 0
- gaps
- 0
- loci tagged
- 600
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 | 540 | 99 | |
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 | 28 (53 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 25 (27 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 29 (27 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 25 (27 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 27 (53 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 26 (53 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 28 (53 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 27 (53 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 25 (27 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 29 (27 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 25 (27 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 28 (53 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 5 (75 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 27 (53 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 26 (53 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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