Full information on isolate SB6442 (id:9504)
Projects
This isolate is a member of the following project:
- Barbier et al_ApplEnvironMicrobiol_2020
- Collection of KpSC genomes studied in "The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples" (PMID: 32005732)
Provenance/primary metadata
- id
- 9504
- isolate
- SB6442
- alias
- MVK-03E096
- sender
- Elodie Barbier, Institut National de Recherche Agronomique (INRA) Dijon, France
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 15 updates show details
- date entered
- 2019-08-08
- datestamp
- 2023-01-13
- taxonomic designation
- K. variicola subsp. variicola
- QC status
- 0000
- isolation year
- 2018
- city
- Auxonne
- country
- France
- continent
- Europe
- source type
- Environment
- host
- Environment
- source details
- roots
- source lab
- persil root
- comments
- Auxonne
Sequence bin
- contigs
- 72
- total length
- 5,427,219 bp
- max length
- 779,673 bp
- mean length
- 75,379 bp
- N50
- 183,706
- L50
- 9
- N90
- 61,566
- L90
- 27
- N95
- 33,715
- L95
- 33
- %GC
- 57.65
- Ns
- 0
- gaps
- 0
- loci tagged
- 656
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 | |||
| MLST | 7 | 7 | 100 | |
| Ribosomal MLST | 53 | 28 | 52 | |
| scgMLST629_S | 629 | 607 | 96 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella variicola | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella variicola | 100% |
Analysis performed: 2022-11-02
Kleborate
- species
- Klebsiella variicola subsp. variicola
- species_match
- strong
- virulence_score
- 0
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- K_locus
- unknown (KL107)
- K_type
- unknown (KL107)
- K_locus_problems
- ?-+*
- K_locus_confidence
- None
- K_locus_identity
- 83.32%
- K_locus_missing_genes
- KL107_05_wzb,KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10,KL107_12,KL107_13,KL107_16_ugd
- O_locus
- OL103
- O_type
- unknown (OL103)
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.93%
- Bla_chr
- LEN-2^
Analysis performed: 2024-03-12; Kleborate v2.3.2
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 |
|---|---|---|---|---|---|
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 405 (33 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1055 (5 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 405 (33 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1055 (5 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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