Full information on isolate SRR3051245 (id:43560)
Provenance/primary metadata
- id
- 43560
- isolate
- SRR3051245
- aliases
- C00026621; SAMN04357413
- 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
- 2011
- city
- Oxford
- country
- UK
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Blood
Sequence bin
- contigs
- 63
- total length
- 5,356,179 bp
- max length
- 430,421 bp
- mean length
- 85,019 bp
- N50
- 206,891
- L50
- 9
- N90
- 63,360
- L90
- 24
- N95
- 39,179
- L95
- 30
- %GC
- 57.24
- Ns
- 395
- gaps
- 4
- loci tagged
- 688
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 | 628 | 99 | |
Analysis
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
- 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
- 98.62%
- Bla_chr
- SHV-1
Analysis performed: 2024-06-01; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_8_17_0_0_0_0_0
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_127_8_17_0 | 7 | 1 |
| 0_0_127_8_17_0_0 | 4 | 1 |
| 0_0_127_8_17_0_0_0 | 2 | 1 |
| 0_0_127_8_17_0_0_0_0 | 1 | 1 |
| 0_0_127_8_17_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_17 | 10 | 1 |
| 0_0_127_8_17_0 | 7 | 1 |
| 0_0_127_8_17_0_0 | 4 | 1 |
| 0_0_127_8_17_0_0_0 | 2 | 1 |
| 0_0_127_8_17_0_0_0_0 | 1 | 1 |
| 0_0_127_8_17_0_0_0_0_0 | 0 | 1 |
Schemes and loci
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Tools
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