Full information on isolate MEZ13_S2 (id:15865)
Projects
This isolate is a member of the following project:
- Ezzat_2021
- Klebsiella from South Africa
Provenance/primary metadata
- id
- 15865
- isolate
- MEZ13_S2
- sender
- Mohamed Ezzat, Zoonosis Science Center, University of Uppsala, Sweden
- curator
- Auto Tagger
- update history
- 13 updates show details
- date entered
- 2021-04-01
- datestamp
- 2023-01-22
- taxonomic designation
- K. variicola subsp. variicola
- isolation year
- 2018
- city
- KwaZulu-Natal
- country
- South Africa
- continent
- Africa
- source type
- Farm Animal
- host
- Chicken
- source lab
- Prof. Dr. Mohamed Ezzat El Zowalaty
- accession number
- PRJNA716986
Sequence bin
- contigs
- 116
- total length
- 5,549,701 bp
- max length
- 335,124 bp
- mean length
- 47,843 bp
- N50
- 185,746
- L50
- 11
- N90
- 62,490
- L90
- 32
- N95
- 30,743
- L95
- 38
- %GC
- 57.53
- Ns
- 391
- gaps
- 4
- loci tagged
- 689
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 | 618 | 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
- 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
- unknown (KL43)
- K_type
- unknown (K43)
- K_locus_problems
- ?-+*
- K_locus_confidence
- None
- K_locus_identity
- 98.46%
- K_locus_missing_genes
- KL43_08_wcuO,KL43_13_wcuV,KL43_15_wcpZ,KL43_17_manC,KL43_18_manB
- O_locus
- O3/O3a
- O_type
- O3/O3a
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 99.25%
- O_locus_missing_genes
- O3/O3a_01_manC,O3/O3a_02_manB
- Bla_chr
- LEN-16^
Analysis performed: 2024-03-23; Kleborate v2.3.2
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 (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 | 1278 (4 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2214 (3 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 | 1278 (4 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2214 (3 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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