Full information on isolate DRR122566 (id:23449)
Provenance/primary metadata
- id
- 23449
- isolate
- DRR122566
- alias
- SAMD00108886
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 8 updates show details
- date entered
- 2023-02-15
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2016
- city
- Surin
- country
- Thailand
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Unknown
Sequence bin
- contigs
- 44
- total length
- 5,480,669 bp
- max length
- 942,330 bp
- mean length
- 124,561 bp
- N50
- 426,487
- L50
- 5
- N90
- 86,650
- L90
- 15
- N95
- 45,422
- L95
- 19
- %GC
- 57.16
- Ns
- 487
- gaps
- 5
- loci tagged
- 706
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 | 627 | 99 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella pneumoniae | Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2023-12-14
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 4
- resistance_score
- 2
- num_resistance_classes
- 7
- num_resistance_genes
- 8
- Yersiniabactin
- ybt 14; ICEKp5
- YbST
- 376-1LV
- CbST
- 0
- Aerobactin
- iuc 5
- AbST
- 61-3LV
- SmST
- 0
- RmST
- 0
- wzi
- wzi104
- K_locus
- KL51
- K_type
- K51
- K_locus_confidence
- High
- K_locus_identity
- 99.39%
- K_locus_missing_genes
- KL51_14_wcoZ
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.44%
- AGly_acquired
- aac(6')-Ib;rmtF
- Flq_acquired
- qnrS1
- MLS_acquired
- ermB.v1*
- Phe_acquired
- catA1^
- Rif_acquired
- arr-2
- Bla_acquired
- TEM-1D.v1^
- Bla_Carb_acquired
- OXA-232
- Bla_chr
- SHV-1^
- Omp_mutations
- OmpK35-30%;OmpK36TD
- Flq_mutations
- GyrA-83I;ParC-80I
- spurious_resistance_hits
- CTX-M-114?-0%
- ybtS
- 4
- ybtX
- 4
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 8
- irp1
- 8*
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
- iucA
- 29
- iucB
- 17
- iucC
- 28
- iucD
- 35
- iutA
- 61
Analysis performed: 2024-03-22; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_88_0_0_0_26_0_0_0
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_88_0_0_0 | 7 | 463 |
| 0_0_88_0_0_0_26 | 4 | 35 |
| 0_0_88_0_0_0_26_0 | 2 | 33 |
| 0_0_88_0_0_0_26_0_0 | 1 | 18 |
| 0_0_88_0_0_0_26_0_0_0 | 0 | 18 |
| 0 | 610 | 38011 |
| 0_0 | 585 | 38011 |
| 0_0_88 | 190 | 519 |
| 0_0_88_0 | 43 | 509 |
| 0_0_88_0_0 | 10 | 498 |
| 0_0_88_0_0_0 | 7 | 463 |
| 0_0_88_0_0_0_26 | 4 | 35 |
| 0_0_88_0_0_0_26_0 | 2 | 33 |
| 0_0_88_0_0_0_26_0_0 | 1 | 18 |
| 0_0_88_0_0_0_26_0_0_0 | 0 | 18 |
Schemes and loci
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Tools
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