Full information on isolate ERR2796978 (id:27781)
Provenance/primary metadata
- id
- 27781
- isolate
- ERR2796978
- aliases
- kpneu035; SAMEA4916100
- 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
- Unknown
- country
- Switzerland
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Hospital
Sequence bin
- contigs
- 144
- total length
- 5,492,985 bp
- max length
- 297,054 bp
- mean length
- 38,146 bp
- N50
- 94,106
- L50
- 19
- N90
- 27,004
- L90
- 59
- N95
- 14,907
- L95
- 73
- %GC
- 57.19
- Ns
- 596
- gaps
- 6
- 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
- 8
- num_resistance_genes
- 10
- Yersiniabactin
- ybt 14; ICEKp5 (truncated)
- YbST
- 376-1LV
- 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
- 99.36%
- K_locus_missing_genes
- KL51_07_wcaJ,KL51_09_wzy,KL51_11_wcpA,KL51_12_wzx,KL51_13,KL51_14_wcoZ
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 98.42%
- O_locus_missing_genes
- O1/O2v2_03_wbbM,O1/O2v2_10_gmlA
- AGly_acquired
- aac(6')-Ib;aadA2^;rmtF
- MLS_acquired
- ermB.v1*;mphA
- 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;GyrA-87N;ParC-80I
- truncated_resistance_hits
- CTX-M-15?-0%
- spurious_resistance_hits
- catA1*?-0%
- ybtS
- 4
- ybtX
- 4
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 8
- irp1
- 8*-55%
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
- iucA
- 29*
- iucB
- 17
- iucC
- 28
- iucD
- 35
- iutA
- 61
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_8_1_0
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: