Full information on isolate SB6456 (id:9516)
Projects
Provenance/primary metadata
- id
- 9516
- isolate
- SB6456
- alias
- MVK-03E122
- 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. pneumoniae
- QC status
- 0000
- isolation year
- 2018
- city
- Bourgogne-Franche-Comté region
- country
- France
- continent
- Europe
- source type
- Environment
- host
- Environment
- source details
- leaves
- other source info
- Organic vegetable farm-Sample 5 - salad leaves
- source lab
- INRAE Dijon
Sequence bin
- method
- Illumina
- contigs
- 55
- total length
- 5,030,401 bp
- max length
- 692,708 bp
- mean length
- 91,462 bp
- N50
- 178,312
- L50
- 7
- N90
- 64,127
- L90
- 25
- N95
- 37,489
- L95
- 30
- %GC
- 57.92
- Ns
- 0
- gaps
- 0
- loci tagged
- 700
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 | 627 | 99 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella pneumoniae | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2022-11-02
Kleborate
- species
- Klebsiella pneumoniae
- 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
- wzi
- wzi490
- K_locus
- unknown (KL50)
- K_type
- unknown (K50)
- K_locus_problems
- -+*
- K_locus_confidence
- None
- K_locus_identity
- 92.34%
- K_locus_missing_genes
- KL50_05_wbaZ,KL50_06_wbaP,KL50_07_wcuU,KL50_08_wcuH,KL50_09_wzx,KL50_10
- O_locus
- O1/O2v1
- O_type
- O2a
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.53%
- Bla_chr
- SHV-1
Analysis performed: 2024-03-12; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_22_58_0_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL17
- Clonal group
- CG11545
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 (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 | 4 (706 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2620 (2 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 | 4 (706 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2620 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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