Full information on isolate ERR971952 (id:58973)
Projects
This isolate is a member of the following project:
- Musicha et al. 2019
- Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages (PMID: 30778540)
Provenance/primary metadata
- id
- 58973
- isolate
- ERR971952
- sender
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 3 updates show details
- date entered
- 2024-03-21
- datestamp
- 2024-03-22
- taxonomic designation
- K. pneumoniae
- isolation year
- 2006
- city
- Blantyre
- country
- Malawi
- continent
- Africa
- source type
- Human
- host
- Human
- source details
- Blood
- source lab
- Queen Elizabeth Central Hospital, Blantyre, Malawi
- comments
- Musicha 2019
- accession number
- ERR971952
Sequence bin
- contigs
- 97
- total length
- 5,596,559 bp
- max length
- 488,294 bp
- mean length
- 57,697 bp
- N50
- 254,983
- L50
- 8
- N90
- 49,208
- L90
- 27
- N95
- 26,012
- L95
- 35
- %GC
- 56.93
- Ns
- 276
- gaps
- 232
- 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 | 625 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 1
- resistance_score
- 1
- num_resistance_classes
- 7
- num_resistance_genes
- 12
- Yersiniabactin
- ybt 9; ICEKp3
- YbST
- 183
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi137
- K_locus
- KL17
- K_type
- K17
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 100.00%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.03%
- AGly_acquired
- aac(3)-IIa.v1^;aac(6')-Ib'.v1;aadA*;aph3-Ia.v1^;strA.v1;strB.v1
- Phe_acquired
- catII.2*
- Sul_acquired
- sul2
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- OXA-9.v1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-1^
- Omp_mutations
- OmpK35-17%
- Flq_mutations
- GyrA-83Y;GyrA-87N;ParC-80I
- ybtS
- 5
- ybtX
- 11
- ybtQ
- 6
- ybtP
- 5
- ybtA
- 1
- irp2
- 25
- irp1
- 37
- ybtU
- 9
- ybtT
- 5
- ybtE
- 5
- fyuA
- 11
Analysis performed: 2024-04-30; Kleborate v2.3.2
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: