Full information on isolate SRR16078917 (id:38141)
Provenance/primary metadata
- id
- 38141
- isolate
- SRR16078917
- alias
- SAMN21590786
- 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
- 0
- city
- Unknown
- country
- Singapore
- continent
- Asia
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
Sequence bin
- contigs
- 91
- total length
- 5,684,087 bp
- max length
- 498,588 bp
- mean length
- 62,463 bp
- N50
- 213,352
- L50
- 8
- N90
- 46,276
- L90
- 30
- N95
- 27,898
- L95
- 37
- %GC
- 56.96
- Ns
- 990
- gaps
- 10
- 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
- 4
- resistance_score
- 2
- num_resistance_classes
- 10
- num_resistance_genes
- 17
- Yersiniabactin
- ybt 14; ICEKp5
- YbST
- 376
- CbST
- 0
- Aerobactin
- iuc 5
- AbST
- 61-3LV
- SmST
- 0
- RmST
- 0
- wzi
- wzi104
- K_locus
- unknown (KL51)
- K_type
- unknown (K51)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 99.38%
- K_locus_missing_genes
- KL51_07_wcaJ,KL51_09_wzy,KL51_10_wcuF,KL51_14_wcoZ
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.44%
- AGly_acquired
- aac(6')-Ib;aadA2^;armA;rmtF
- Flq_acquired
- qnrS1
- MLS_acquired
- ermB.v1*;mphA;mphE.v2
- Phe_acquired
- catA1^
- Rif_acquired
- arr-2
- Sul_acquired
- sul1
- Tmt_acquired
- dfrA12
- Bla_acquired
- CMY-4.v1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_Carb_acquired
- NDM-1;OXA-181
- Omp_mutations
- OmpK35-30%;OmpK36TD
- Flq_mutations
- GyrA-83I;ParC-80I
- spurious_resistance_hits
- SHV-129?-73%;msrE*?-77%
- ybtS
- 4
- ybtX
- 4
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 8
- irp1
- 8
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
- iucA
- 29
- iucB
- 17
- iucC
- 28
- iucD
- 35
- iutA
- 61
Analysis performed: 2024-04-11; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_88_0_0_0_0_1_3_0
Schemes and loci
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Tools
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