Full information on isolate SRR5082481 (id:42384)
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
- 42384
- isolate
- SRR5082481
- aliases
- AH0297_C4PNMANXX_CGAGGCTG-AAGGAGTA_L006; SAMN06112201
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 7 updates show details
- date entered
- 2023-02-15
- datestamp
- 2025-05-30
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2014
- city
- Melbourne
- country
- Australia
- continent
- Oceania
- source type
- Human
- host
- Human
- source details
- Rectal swab
Sequence bin
- method
- Unknown
- contigs
- 113
- total length
- 5,563,624 bp
- max length
- 565,489 bp
- mean length
- 49,236 bp
- N50
- 214,960
- L50
- 9
- N90
- 47,087
- L90
- 30
- N95
- 18,466
- L95
- 40
- %GC
- 57.28
- Ns
- 1262
- gaps
- 13
- loci tagged
- 3,413
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 | 626 | 99 | |
| Kpn_cgMLST | 2752 | 2727 | 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
- wzi281
- K_locus
- KL38
- K_type
- K38
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.68%
- O_locus
- O3b
- O_type
- O3b
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.14%
- Bla_chr
- SHV-36^
- SHV_mutations
- 35Q
Analysis performed: 2024-04-12; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_51_2_0_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL1738
- Clonal group
- CG14579
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: