Full information on isolate 997 (id:4053)
Projects
Provenance/primary metadata
- id
- 4053
- isolate
- 997
- alias
- 58837
- sender
- Rebekah Martin, The University of Michigan, Department of Pathology, Dr. Michael Bachman lab,USA,
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 19 updates show details
- date entered
- 2016-07-08
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- isolation year
- 2014
- city
- Ann Arbor, MI
- country
- USA
- continent
- North America
- source type
- Human
- host
- Human
- source details
- Stool
- other source info
- Same patient as 728
- K type
- wzi-82-K23
- K typing method
- wzi sequencing
Publication (1)
- Martin RM, Cao J, Brisse S, Passet V, Wu W, Zhao L, Malani PN, Rao K, Bachman MA (2016). Molecular Epidemiology of Colonizing and Infecting Isolates of Klebsiella pneumoniae. mSphere 1:
Sequence bin
- contigs
- 194
- total length
- 5,728,839 bp
- max length
- 1,291,619 bp
- mean length
- 29,531 bp
- N50
- 426,408
- L50
- 4
- N90
- 75,499
- L90
- 15
- N95
- 27,673
- L95
- 21
- %GC
- 56.96
- Ns
- 1264
- gaps
- 23
- loci tagged
- 3,958
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
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella pneumoniae | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2022-11-02
Kleborate
- species
- Klebsiella pneumoniae
- 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
- wzi
- wzi82
- K_locus
- KL23
- K_type
- K23
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.95%
- O_locus
- O1/O2v2
- O_type
- O2afg
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.45%
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
Analysis performed: 2024-02-26; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_22_8_4_1_0_0_0_0
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 (13440 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13419 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 4 (588 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 63 (13 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13440 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13419 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 4 (588 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 63 (13 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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