Full information on isolate GCA_900084675.1 (id:46775)
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
- 46775
- isolate
- GCA_900084675.1
- alias
- k142b
- 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. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- isolation year
- 0
- city
- Unknown
- country
- UK
- continent
- Europe
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMEA2273523
Sequence bin
- contigs
- 44
- total length
- 5,519,319 bp
- max length
- 737,568 bp
- mean length
- 125,440 bp
- N50
- 334,713
- L50
- 6
- N90
- 81,245
- L90
- 19
- N95
- 50,363
- L95
- 24
- %GC
- 57.08
- Ns
- 4055
- gaps
- 17
- loci tagged
- 691
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 | 628 | 99 |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 1
- num_resistance_classes
- 7
- num_resistance_genes
- 7
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi96
- K_locus
- KL38
- K_type
- K38
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.69%
- O_locus
- O3b
- O_type
- O3b
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.30%
- AGly_acquired
- aac(3)-IId^
- Sul_acquired
- sul1
- Tet_acquired
- tet(D)
- Tmt_acquired
- dfrA5
- Bla_acquired
- TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15;SHV-129?
- SHV_mutations
- 238S;240K;35Q
- Omp_mutations
- OmpK35-10%
- Flq_mutations
- GyrA-83Y
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 | 5 (350 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 47 (98 isolates) |
klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 48 (7 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 | 5 (350 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 47 (98 isolates) |
klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 48 (7 isolates) |
klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 50 (1 isolate) |
klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 51 (1 isolate) |
klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 52 (1 isolate) |
klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 53 (1 isolate) |
klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 53 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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