Full information on isolate ERR971965 (id:58982)
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
- 58982
- isolate
- ERR971965
- 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
- 2005
- 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
- ERR971965
Sequence bin
- contigs
- 60
- total length
- 5,377,733 bp
- max length
- 639,074 bp
- mean length
- 89,629 bp
- N50
- 257,792
- L50
- 8
- N90
- 86,387
- L90
- 23
- N95
- 77,621
- L95
- 26
- %GC
- 57.45
- Ns
- 103
- gaps
- 87
- loci tagged
- 703
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 | 629 | 100 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 1
- resistance_score
- 0
- num_resistance_classes
- 5
- num_resistance_genes
- 6
- Yersiniabactin
- ybt 10; ICEKp4
- YbST
- 78
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi101
- K_locus
- KL24
- K_type
- K24
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.02%
- O_locus
- O1/O2v1
- O_type
- O2a
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.76%
- AGly_acquired
- strA.v1*;strB.v1*
- Phe_acquired
- catII.2*
- Sul_acquired
- sul2
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- TEM-1D.v1^
- Bla_chr
- SHV-1
- ybtS
- 3
- ybtX
- 12
- ybtQ
- 4
- ybtP
- 11
- ybtA
- 3
- irp2
- 21
- irp1
- 18
- ybtU
- 3
- ybtT
- 10
- ybtE
- 16
- fyuA
- 2
Analysis performed: 2024-04-30; Kleborate v2.3.2
Schemes and loci
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Tools
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Analysis: