Full information on isolate ERR3162592 (id:26959)
Provenance/primary metadata
- id
- 26959
- isolate
- ERR3162592
- aliases
- BA3081; SAMEA5232560
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 6 updates show details
- date entered
- 2023-02-15
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2017
- city
- Unknown
- country
- India
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Blood
Sequence bin
- contigs
- 295
- total length
- 5,581,499 bp
- max length
- 229,062 bp
- mean length
- 18,921 bp
- N50
- 46,295
- L50
- 36
- N90
- 10,886
- L90
- 123
- N95
- 4,758
- L95
- 160
- %GC
- 57.20
- Ns
- 3146
- gaps
- 40
- loci tagged
- 701
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 | 623 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 4
- resistance_score
- 2
- num_resistance_classes
- 9
- num_resistance_genes
- 11
- Yersiniabactin
- ybt 14; ICEKp5
- YbST
- 376
- CbST
- 0
- Aerobactin
- iuc unknown
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi104
- K_locus
- unknown (KL107)
- K_type
- unknown (KL107)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 87.73%
- K_locus_missing_genes
- KL107_05_wzb,KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10,KL107_12,KL107_13,KL107_14,KL107_15
- O_locus
- unknown (O1/O2v1)
- O_type
- unknown (O2a)
- O_locus_problems
- ?-
- O_locus_confidence
- None
- O_locus_identity
- 95.92%
- O_locus_missing_genes
- O1/O2v1_01_wzm,O1/O2v1_07_kfoC
- AGly_acquired
- aac(6')-Ib;aadA2^;rmtF
- Flq_acquired
- qnrS1
- MLS_acquired
- mphA
- Phe_acquired
- catA1^
- Rif_acquired
- arr-2
- Sul_acquired
- sul1
- Tmt_acquired
- dfrA12
- Bla_acquired
- TEM-1D.v1^
- Bla_Carb_acquired
- OXA-232
- Bla_chr
- SHV-1^
- Omp_mutations
- OmpK35-30%;OmpK36TD
- Flq_mutations
- GyrA-83I;ParC-80I
- truncated_resistance_hits
- CTX-M-15?-0%
- 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
- iucD
- 35
- iutA
- 61*-0%
- spurious_virulence_hits
- iucC_35*-70%
Analysis performed: 2024-03-27; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_88_0_0_0_0_0_2_0
Schemes and loci
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Tools
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