Full information on isolate SB6448 (id:9510)
Projects
Provenance/primary metadata
- id
- 9510
- isolate
- SB6448
- alias
- MVK-03E112
- sender
- Elodie Barbier, Institut National de Recherche Agronomique (INRA) Dijon, France
- curator
- Carla Rodrigues, Institut Pasteur, France (E-mail: carla.parada-rodrigues@pasteur.fr)
- update history
- 20 updates show details
- date entered
- 2019-08-08
- datestamp
- 2025-12-05
- taxonomic designation
- K. variicola subsp. variicola
- QC status
- 0000
- isolation year
- 2018
- city
- Bourgogne-Franche-Comté region
- country
- France
- continent
- Europe
- source type
- Environment
- host
- Environment
- source details
- roots
- other source info
- Organic vegetable farm-Sample 18 - basil roots
- source lab
- INRAE Dijon
Sequence bin
- method
- Illumina
- contigs
- 46
- total length
- 5,467,119 bp
- max length
- 685,202 bp
- mean length
- 118,851 bp
- N50
- 345,910
- L50
- 6
- N90
- 83,339
- L90
- 22
- N95
- 65,674
- L95
- 25
- %GC
- 57.60
- Ns
- 0
- gaps
- 0
- loci tagged
- 692
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 | 53 | 100 | |
| scgMLST629_S | 629 | 617 | 98 | |
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
- 81.41%
- K_locus_missing_genes
- KL107_05_wzb,KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10,KL107_11_gnd,KL107_12,KL107_13,KL107_14,KL107_15
- O_locus
- O3/O3a
- O_type
- O3/O3a
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 99.39%
- O_locus_missing_genes
- O3/O3a_01_manC,O3/O3a_02_manB
- Bla_chr
- LEN-13
Analysis performed: 2025-05-14; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 1_0_22_1_0_0_0_0_0_0
- Phylogroup
- Kp3
- Sublineage
- SL2594
- Clonal group
- CG14363
Similar isolates (determined by classification schemes)
Some groups only contain this isolate. Show single groups
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 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 635 (19 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 635 (19 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2619 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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