Full information on isolate GCA_001904015.4 (id:48169)
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
- 48169
- isolate
- GCA_001904015.4
- alias
- CRK0114
- sender
- Mélanie Hennart, Institut Pasteur
- curator
- Auto Tagger
- update history
- 4 updates show details
- date entered
- 2023-03-23
- datestamp
- 2023-04-14
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- isolation year
- 0
- city
- Unknown
- country
- USA
- continent
- North America
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMN05956140
Sequence bin
- contigs
- 75
- total length
- 5,509,044 bp
- max length
- 714,212 bp
- mean length
- 73,454 bp
- N50
- 304,316
- L50
- 7
- N90
- 62,903
- L90
- 22
- N95
- 34,789
- L95
- 28
- %GC
- 57.25
- Ns
- 0
- gaps
- 0
- loci tagged
- 686
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 | 626 | 99 |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 0
- resistance_score
- 2
- num_resistance_classes
- 7
- num_resistance_genes
- 11
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi100
- K_locus
- KL10
- K_type
- K10
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 96.76%
- O_locus
- unknown (O3/O3a)
- O_type
- unknown (O3/O3a)
- O_locus_problems
- ?-
- O_locus_confidence
- None
- O_locus_identity
- 98.36%
- O_locus_missing_genes
- O3/O3a_03_wzm,O3/O3a_04_wzt,O3/O3a_05_wbdD,O3/O3a_06_wbdA,O3/O3a_07_wbdB
- AGly_acquired
- aac(6')-Ib-cr.v2^;aadA17*;ant(2'')-Ia;aph3-Ia.v1*?
- MLS_acquired
- mphA
- Phe_acquired
- catB3.v2
- Rif_acquired
- arr-3
- Sul_acquired
- sul1
- Bla_acquired
- OXA-1;TEM-1D.v1^
- Bla_Carb_acquired
- KPC-4
- Bla_chr
- SHV-1^
- Omp_mutations
- OmpK35-18%
Analysis performed: 2024-04-16; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_46_5_1_0_0_0_0_0
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 (13437 isolates) |
klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 52 (57 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 348 (7 isolates) |
klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 559 (2 isolates) |
klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 623 (2 isolates) |
klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 744 (2 isolates) |
klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 889 (2 isolates) |
klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 1026 (2 isolates) |
klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13437 isolates) |
klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 52 (57 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 348 (7 isolates) |
klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 559 (2 isolates) |
klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 623 (2 isolates) |
klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 744 (2 isolates) |
klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 889 (2 isolates) |
klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 1026 (2 isolates) |
klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 1233 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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