Full information on isolate GCA_900004985.1 (id:46766)
Projects
This isolate is a member of the following project:
- Hennart_et_al_2022_full_collection
- Collection of genomes from the paper "A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains" | PMID: 35700230
Provenance/primary metadata
- id
- 46766
- isolate
- GCA_900004985.1
- sender
- Mélanie Hennart, Institut Pasteur
- curator
- Auto Tagger
- update history
- 3 updates show details
- date entered
- 2023-03-23
- datestamp
- 2023-03-24
- taxonomic designation
- K. variicola subsp. variicola
- phylogroup from ST
- Kp3 (7 loci)
- isolation year
- 0
- city
- Unknown
- country
- Malawi
- continent
- Africa
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMEA3735820
Sequence bin
- contigs
- 75
- total length
- 5,691,516 bp
- max length
- 518,614 bp
- mean length
- 75,887 bp
- N50
- 154,183
- L50
- 12
- N90
- 47,099
- L90
- 37
- N95
- 30,360
- L95
- 44
- %GC
- 56.95
- Ns
- 558
- gaps
- 55
- loci tagged
- 677
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 | 616 | 97 | |
Analysis
Kleborate
- species
- Klebsiella variicola subsp. variicola
- species_match
- strong
- QC_warnings
- ambiguous_bases
- 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
- KL81
- K_type
- K81
- K_locus_problems
- ?-*
- K_locus_confidence
- Good
- K_locus_identity
- 92.00%
- K_locus_missing_genes
- KL81_17_rmlB,KL81_18_rmlA,KL81_20_rmlC
- O_locus
- unknown (OL101)
- O_type
- unknown (OL101)
- O_locus_problems
- ?-
- O_locus_confidence
- None
- O_locus_identity
- 91.28%
- O_locus_missing_genes
- OL101_01_rfbB,OL101_02_rfbA,OL101_04_rfbC,OL101_09_glycosylhydrolase
- Bla_chr
- LEN-16^
- Omp_mutations
- OmpK35-20%
Analysis performed: 2024-04-17; Kleborate v2.3.2
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 (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 | 19 (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 | 19 (5 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 39 (1 isolate) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 39 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 40 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 41 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 42 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 43 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 43 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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