Full information on isolate SRR12509107 (id:30943)
Provenance/primary metadata
- id
- 30943
- isolate
- SRR12509107
- alias
- SAMN15868439
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 7 updates show details
- date entered
- 2023-02-15
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2016
- city
- Northeast
- country
- USA
- continent
- North America
- source type
- Human
- host
- Human
- source details
- urine
Sequence bin
- contigs
- 158
- total length
- 5,855,150 bp
- max length
- 359,145 bp
- mean length
- 37,058 bp
- N50
- 129,104
- L50
- 15
- N90
- 26,236
- L90
- 56
- N95
- 16,624
- L95
- 71
- %GC
- 56.63
- Ns
- 601
- gaps
- 7
- loci tagged
- 718
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
- 2
- resistance_score
- 2
- num_resistance_classes
- 8
- num_resistance_genes
- 11
- Yersiniabactin
- ybt 17; ICEKp10
- YbST
- 289
- Colibactin
- clb 3
- CbST
- 17-1LV
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi7
- K_locus
- KL7
- K_type
- K7
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 98.45%
- K_locus_missing_genes
- KL7_08_wckC,KL7_09_wcuC,KL7_10_wzy
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 98.59%
- O_locus_missing_genes
- O1/O2v1_06_wbbO
- AGly_acquired
- aac(6')-Ib'.v1*;aadA*;strA.v1^;strB.v1
- Phe_acquired
- floR.v2*
- Sul_acquired
- sul2
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- OXA-9.v1;TEM-1D.v1^
- Bla_ESBL_acquired
- SHV-12
- Bla_Carb_acquired
- KPC-3
- SHV_mutations
- 238S;240K;35Q
- Flq_mutations
- GyrA-83F;GyrA-87G;ParC-80I
- ybtS
- 6
- ybtX
- 15
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 11
- irp2
- 28
- irp1
- 26
- ybtU
- 2
- ybtT
- 11
- ybtE
- 4
- fyuA
- 2
- clbA
- 2
- clbB
- 31*
- clbC
- 2
- clbD
- 2
- clbE
- 2
- clbF
- 2
- clbG
- 2
- clbH
- 8
- clbI
- 2
- clbL
- 2
- clbM
- 2
- clbN
- 2
- clbO
- 2
- clbP
- 2
- clbQ
- 2
Analysis performed: 2024-04-06; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_5_0_1_0_3_0_0
Schemes and loci
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Tools
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