Full information on isolate SRR2098701 (id:46430)
Provenance/primary metadata
- id
- 46430
- isolate
- SRR2098701
- aliases
- Kpn_0006; SAMN03853225
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 5 updates show details
- date entered
- 2023-02-15
- datestamp
- 2023-04-17
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2012
- city
- Flagstaff, AZ
- country
- USA
- continent
- North America
- source type
- Food
- host
- Food
- source details
- Retail chicken
Sequence bin
- contigs
- 103
- total length
- 5,407,667 bp
- max length
- 339,949 bp
- mean length
- 52,502 bp
- N50
- 89,637
- L50
- 18
- N90
- 34,095
- L90
- 57
- N95
- 21,004
- L95
- 66
- %GC
- 57.26
- Ns
- 628
- gaps
- 24
- loci tagged
- 683
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 | 623 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 1
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 14; ICEKp5
- YbST
- 145-2LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi7
- K_locus
- KL7
- K_type
- K7
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 98.53%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.61%
- Bla_chr
- SHV-1
- ybtS
- 4
- ybtX
- 4
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 288*
- irp1
- 306*
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
Analysis performed: 2024-04-16; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_8_20_0_0_0_0_0
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_127_8_20_0 | 7 | 1 |
| 0_0_127_8_20_0_0 | 4 | 1 |
| 0_0_127_8_20_0_0_0 | 2 | 1 |
| 0_0_127_8_20_0_0_0_0 | 1 | 1 |
| 0_0_127_8_20_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_20 | 10 | 1 |
| 0_0_127_8_20_0 | 7 | 1 |
| 0_0_127_8_20_0_0 | 4 | 1 |
| 0_0_127_8_20_0_0_0 | 2 | 1 |
| 0_0_127_8_20_0_0_0_0 | 1 | 1 |
| 0_0_127_8_20_0_0_0_0_0 | 0 | 1 |
Schemes and loci
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Tools
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