Full information on isolate SRR5082475 (id:42524)
Projects
This isolate is a member of the following project:
- Gorrie et al. 2017
- Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients (PMID: 28369261)
Provenance/primary metadata
- id
- 42524
- isolate
- SRR5082475
- aliases
- AH0148_C4PNMANXX_TAGGCATG-AAGGAGTA_L006; SAMN06112198
- 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
- 2013
- city
- Melbourne
- country
- Australia
- continent
- Oceania
- source type
- Human
- host
- Human
- source details
- Rectal swab
Sequence bin
- contigs
- 69
- total length
- 5,377,965 bp
- max length
- 576,512 bp
- mean length
- 77,942 bp
- N50
- 322,957
- L50
- 7
- N90
- 99,443
- L90
- 18
- N95
- 41,130
- L95
- 22
- %GC
- 57.41
- Ns
- 1102
- gaps
- 13
- loci tagged
- 689
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 | 629 | 100 | |
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 4; plasmid
- YbST
- 64
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi316
- K_locus
- KL6
- K_type
- K6
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.63%
- O_locus
- O1/O2v1
- O_type
- O2a
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.42%
- Bla_chr
- SHV-1^
- ybtS
- 23
- ybtX
- 27
- ybtQ
- 30
- ybtP
- 18
- ybtA
- 13
- irp2
- 110
- irp1
- 61
- ybtU
- 9
- ybtT
- 18
- ybtE
- 26
- fyuA
- 35
Analysis performed: 2024-04-12; Kleborate v2.3.2
Schemes and loci
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Tools
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