Full information on isolate SRR16308461 (id:38472)
Provenance/primary metadata
- id
- 38472
- isolate
- SRR16308461
- alias
- SAMN22240580
- 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
- 2019
- city
- University Hospital Brno, Brno
- country
- Czech Republic
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Unknown
Sequence bin
- contigs
- 102
- total length
- 5,546,138 bp
- max length
- 855,166 bp
- mean length
- 54,374 bp
- N50
- 303,154
- L50
- 7
- N90
- 36,545
- L90
- 24
- N95
- 19,814
- L95
- 35
- %GC
- 57.22
- Ns
- 595
- gaps
- 6
- loci tagged
- 687
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
- 0
- resistance_score
- 1
- num_resistance_classes
- 7
- num_resistance_genes
- 11
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi7
- K_locus
- KL7
- K_type
- K7
- K_locus_problems
- ?
- K_locus_confidence
- Good
- K_locus_identity
- 98.54%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.61%
- AGly_acquired
- aac(3)-IIa.v1^;aac(6')-Ib-cr.v2;strA.v1^;strB.v1
- Flq_acquired
- qnrB1.v2^
- Phe_acquired
- CatB4.v1?
- Sul_acquired
- sul2
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- OXA-1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-1
Analysis performed: 2024-04-11; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_10_0_0_1_0_0_0
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_127_10_0_0 | 7 | 4 |
| 0_0_127_10_0_0_1 | 4 | 4 |
| 0_0_127_10_0_0_1_0 | 2 | 4 |
| 0_0_127_10_0_0_1_0_0 | 1 | 4 |
| 0_0_127_10_0_0_1_0_0_0 | 0 | 4 |
| 0 | 610 | 37702 |
| 0_0 | 585 | 37702 |
| 0_0_127 | 190 | 105 |
| 0_0_127_10 | 43 | 20 |
| 0_0_127_10_0 | 10 | 4 |
| 0_0_127_10_0_0 | 7 | 4 |
| 0_0_127_10_0_0_1 | 4 | 4 |
| 0_0_127_10_0_0_1_0 | 2 | 4 |
| 0_0_127_10_0_0_1_0_0 | 1 | 4 |
| 0_0_127_10_0_0_1_0_0_0 | 0 | 4 |
Schemes and loci
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Tools
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