Full information on isolate SB5387_g_80X (id:58856)
Provenance/primary metadata
- id
- 58856
- isolate
- SB5387_g_80X
- alias
- SB5387
- sender
- Chiara Crestani, Pasteur Institute, France
- curator
- Auto Tagger
- update history
- 2 updates show details
- embargo history
- show details
- date entered
- 2024-02-29
- datestamp
- 2024-02-29
- taxonomic designation
- K. variicola subsp. tropica
- phylogroup from ST
- Kp5
- isolation year
- 2015
- city
- Unknown
- country
- Madagascar
- continent
- Africa
- source type
- Human
- host
- pregnant woman
- source details
- Fecal sample
- other source info
- carriage
- source lab
- Institut Pasteur of Madagascar
- comments
- Nanopore_R10
Sequence bin
- method
- Unknown
- contigs
- 2
- total length
- 5,801,841 bp
- max length
- 5,567,994 bp
- mean length
- 2,900,921 bp
- N50
- 5,567,994
- L50
- 1
- N90
- 5,567,994
- L90
- 1
- N95
- 5,567,994
- L95
- 1
- %GC
- 56.89
- Ns
- 0
- gaps
- 0
- loci tagged
- 613
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 | |||
| scgMLST629_S | 629 | 613 | 97 | |
Analysis
Kleborate
- species
- Klebsiella variicola subsp. tropica
- species_match
- strong
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- virulence_score
- 0
- Bla_chr
- LEN-39
- Omp_mutations
- OmpK36:p.Ala183fs
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Ciprofloxacin_prediction
- wildtype S
- Ciprofloxacin_profile_support
- 90.99% S (N=5168/5680)
- Ciprofloxacin_profile
- 0^ QRDR, 0 PMQR, 0 aac(6`)-Ib-cr
- Ciprofloxacin_MIC_prediction
- 0.25 mg/L [0.25-0.25]
- wzi
- wzi509
- K_locus
- KL124
- K_type
- Capsule null
- K_locus_confidence
- Typeable
- K_locus_problems
- !
- K_locus_identity
- 98.49%
- O_locus
- OL13
- O_type
- O13
- O_locus_confidence
- Typeable
- O_locus_identity
- 97.52%
Analysis performed: 2026-03-02; Kleborate v3.2.4
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 1_1_8_0_0_0_0_0_0_0
- Phylogroup
- Kp5
- Sublineage
- SL2466
- Clonal group
- CG2466
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 | 6 (52 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 25 (32 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 25 (32 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 25 (32 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 25 (32 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 25 (32 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 25 (32 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 25 (32 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 25 (32 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 6 (52 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 25 (32 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 25 (32 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 25 (32 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 25 (32 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 25 (32 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 25 (32 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 25 (32 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 25 (32 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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