Full information on isolate TC112 (id:1243)
Provenance/primary metadata
- id
- 1243
- isolate
- TC112
- alias
- CP084036
- biosample
- SAMN21173716
- accession number
- GCF_023023725.1
- clade
- P1
- species
- borgpetersenii
- serogroup
- Unknown
- serovar
- Hardjobovis
- isolation year
- 2016
- sequencing year
- 2021
- world region
- Northern America
- country
- USA
- host
- bovine
- sample type
- Urine
- source lab
- GenBank
- province
- Iowa
- sender
- Vallier SORDOILLET, CNR Leptospirose PASTEUR
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 18 updates show details
- date entered
- 2022-06-27
- datestamp
- 2024-07-15
Publication (1)
- Putz EJ, Bayles DO, Alt DP, Nally JE (2022). Complete Genome Sequence of Four Strains of Leptospira borgpetersenii serovar Hardjo isolated from Cattle in the Central United States. J Genomics 10:45-48
Sequence bin
- contigs
- 2
- total length
- 3,902,946 bp
- max length
- 3,585,599 bp
- mean length
- 1,951,473 bp
- N50
- 3,585,599
- L50
- 1
- N90
- 3,585,599
- L90
- 1
- N95
- 317,347
- L95
- 2
- %GC
- 40.22
- Ns
- 0
- gaps
- 0
- loci tagged
- 621
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 | 72 (38 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 66 (11 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 69 (38 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 127 (8 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 64 (11 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 63 (11 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 117 (8 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 60 (11 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 59 (11 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 58 (16 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 74 (38 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 53 (20 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 69 (38 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 65 (38 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 72 (38 isolates) |
| Test-75 | cgMLST | Single-linkage | 75 | experimental | 66 (11 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 69 (38 isolates) |
| Test-10 | cgMLST | Single-linkage | 10 | experimental | 127 (8 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 64 (11 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 63 (11 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 117 (8 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 60 (11 isolates) |
| Test-220 | cgMLST | Single-linkage | 220 | experimental | 59 (11 isolates) |
| Test-250 | cgMLST | Single-linkage | 250 | experimental | 58 (16 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 74 (38 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 53 (20 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 69 (38 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 65 (38 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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