Full information on isolate NMI4838/16 (id:22999)
Projects
This isolate is a member of the following project:
- Public isolates
- This project contains the isolates that should be publicly available through the public access database.
Provenance/primary metadata
- id
- 22999
- isolate
- NMI4838/16
- sender
- Radek Izdebski, National Medecines Institute Chelmska 30/34 00-725 Warsaw, Poland
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 4 updates show details
- date entered
- 2023-01-16
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- isolation year
- 2016
- city
- Wrocław
- country
- Poland
- continent
- Europe
- source type
- Human
- host
- human
- source details
- BAL
Sequence bin
- contigs
- 109
- total length
- 5,625,051 bp
- max length
- 582,621 bp
- mean length
- 51,606 bp
- N50
- 303,041
- L50
- 7
- N90
- 55,639
- L90
- 23
- N95
- 27,783
- L95
- 30
- %GC
- 57.26
- Ns
- 0
- gaps
- 0
- loci tagged
- 675
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 | 611 | 97 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella pneumoniae | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2023-01-17
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 0
- resistance_score
- 2
- num_resistance_classes
- 3
- num_resistance_genes
- 3
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi22
- K_locus
- KL48
- K_type
- K48
- K_locus_problems
- *
- K_locus_confidence
- High
- K_locus_identity
- 94.76%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 97.99%
- AGly_acquired
- aac(6')-Ib-cr.v2^
- Sul_acquired
- sul1
- Bla_Carb_acquired
- VIM-4
- Bla_chr
- SHV-1
Analysis performed: 2024-03-23; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_8_14_1_2_0_0_0
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_127_8_14_1 | 7 | 1 |
| 0_0_127_8_14_1_2 | 4 | 1 |
| 0_0_127_8_14_1_2_0 | 2 | 1 |
| 0_0_127_8_14_1_2_0_0 | 1 | 1 |
| 0_0_127_8_14_1_2_0_0_0 | 0 | 1 |
| 0 | 610 | 37702 |
| 0_0 | 585 | 37702 |
| 0_0_127 | 190 | 105 |
| 0_0_127_8 | 43 | 30 |
| 0_0_127_8_14 | 10 | 1 |
| 0_0_127_8_14_1 | 7 | 1 |
| 0_0_127_8_14_1_2 | 4 | 1 |
| 0_0_127_8_14_1_2_0 | 2 | 1 |
| 0_0_127_8_14_1_2_0_0 | 1 | 1 |
| 0_0_127_8_14_1_2_0_0_0 | 0 | 1 |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: