Full information on isolate SRR10694558 (id:30260)
Provenance/primary metadata
- id
- 30260
- isolate
- SRR10694558
- alias
- SAMN13523813
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 7 updates show details
- date entered
- 2023-02-15
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2016
- city
- Unknown
- country
- USA
- continent
- North America
- source type
- Farm Animal
- host
- bovine
- source details
- mastitis milk
Sequence bin
- contigs
- 55
- total length
- 5,435,128 bp
- max length
- 546,652 bp
- mean length
- 98,821 bp
- N50
- 268,013
- L50
- 8
- N90
- 65,842
- L90
- 22
- N95
- 39,491
- L95
- 28
- %GC
- 57.29
- Ns
- 308
- gaps
- 4
- loci tagged
- 701
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
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 1
- resistance_score
- 1
- num_resistance_classes
- 2
- num_resistance_genes
- 2
- Yersiniabactin
- ybt 16; ICEKp12
- YbST
- 448-2LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi7
- K_locus
- unknown (KL7)
- K_type
- unknown (K7)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 98.24%
- K_locus_missing_genes
- KL7_07_wcuE,KL7_08_wckC,KL7_09_wcuC,KL7_10_wzy,KL7_11_wckD,KL7_12_wclS,KL7_13_wcuJ,KL7_14_wzx
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.62%
- MLS_acquired
- mphA
- Bla_ESBL_acquired
- CTX-M-1
- Bla_chr
- SHV-1
- ybtS
- 100
- ybtX
- 15
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 11
- irp2
- 346
- irp1
- 23*
- ybtU
- 2
- ybtT
- 11
- ybtE
- 4
- fyuA
- 210
Analysis performed: 2024-04-05; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_8_21_0_0_0_0_0
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_127_8_21_0 | 7 | 1 |
| 0_0_127_8_21_0_0 | 4 | 1 |
| 0_0_127_8_21_0_0_0 | 2 | 1 |
| 0_0_127_8_21_0_0_0_0 | 1 | 1 |
| 0_0_127_8_21_0_0_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_21 | 10 | 1 |
| 0_0_127_8_21_0 | 7 | 1 |
| 0_0_127_8_21_0_0 | 4 | 1 |
| 0_0_127_8_21_0_0_0 | 2 | 1 |
| 0_0_127_8_21_0_0_0_0 | 1 | 1 |
| 0_0_127_8_21_0_0_0_0_0 | 0 | 1 |
Schemes and loci
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Tools
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