Full information on isolate 2-2 (id:407)
Projects
Provenance/primary metadata
- id
- 407
- isolate
- 2-2
- aliases
- 2-2; SB611
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 29 updates show details
- date entered
- 2009-02-10
- datestamp
- 2023-11-22
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0120
- city
- Utrecht
- country
- The Netherlands
- continent
- Europe
- source type
- Environment
- host
- Environment
- source details
- Water
- other source info
- Rijnhauwen bridge
- source lab
- UMCU (Utrecht, NL)
Publication (1)
- Brisse S, Fevre C, Passet V, Issenhuth-Jeanjean S, Tournebize R, Diancourt L, Grimont P (2009). Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS One 4:e4982
Sequence bin
- method
- Illumina
- contigs
- 1,052
- total length
- 11,134,977 bp
- max length
- 171,251 bp
- mean length
- 10,585 bp
- N50
- 41,628
- L50
- 77
- N90
- 7,561
- L90
- 302
- N95
- 3,214
- L95
- 412
- %GC
- 57.00
- Ns
- 0
- gaps
- 0
- loci tagged
- 744
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (fail threshold: 501) | |
| Assembly size | assembly size too large (fail threshold: 6,132,847) | |
| 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 | 619 | 98 | |
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
- QC_warnings
- total_size
- 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
- KL111
- K_type
- unknown (KL111)
- K_locus_problems
- ?
- K_locus_confidence
- Good
- K_locus_identity
- 99.52%
- O_locus
- unknown (OL103)
- O_type
- unknown (OL103)
- O_locus_confidence
- None
- O_locus_identity
- 94.33%
- O_locus_missing_genes
- OL103_01_rmlC,OL103_02_wzm,OL103_03_wzt,OL103_04_hydrolase
- Bla_chr
- SHV-1^;SHV-1^
Analysis performed: 2025-05-08; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_1172_2_0_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL11027
- Clonal group
- CG12448
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_1172_2_0_0 | 7 | 2 |
| 0_0_1172_2_0_0_0 | 4 | 2 |
| 0_0_1172_2_0_0_0_0 | 2 | 2 |
| 0_0_1172_2_0_0_0_0_0 | 1 | 1 |
| 0_0_1172_2_0_0_0_0_0_0 | 0 | 1 |
| 0 | 610 | 41312 |
| 0_0 | 585 | 41312 |
| 0_0_1172 | 190 | 13 |
| 0_0_1172_2 | 43 | 2 |
| 0_0_1172_2_0 | 10 | 2 |
| 0_0_1172_2_0_0 | 7 | 2 |
| 0_0_1172_2_0_0_0 | 4 | 2 |
| 0_0_1172_2_0_0_0_0 | 2 | 2 |
| 0_0_1172_2_0_0_0_0_0 | 1 | 1 |
| 0_0_1172_2_0_0_0_0_0_0 | 0 | 1 |
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 | 1724 (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 | 1724 (2 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 3649 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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