Full information on isolate ERR926436 (id:58962)
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
- 58962
- isolate
- ERR926436
- 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
- 2012
- 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
- ERR926436
Sequence bin
- contigs
- 86
- total length
- 5,453,553 bp
- max length
- 460,939 bp
- mean length
- 63,414 bp
- N50
- 272,266
- L50
- 8
- N90
- 74,884
- L90
- 24
- N95
- 26,211
- L95
- 30
- %GC
- 57.25
- Ns
- 113
- gaps
- 95
- loci tagged
- 699
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
- 1
- resistance_score
- 0
- num_resistance_classes
- 4
- num_resistance_genes
- 9
- Yersiniabactin
- ybt 15; ICEKp11
- YbST
- 273-2LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi14
- K_locus
- KL14
- K_type
- K14
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 99.89%
- K_locus_missing_genes
- KL14_20_manB
- O_locus
- O3b
- O_type
- O3b
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 99.30%
- O_locus_missing_genes
- O3b_02_manB
- AGly_acquired
- aadA2^;aadA5;strA.v1^;strB.v1
- MLS_acquired
- mphA
- Sul_acquired
- sul1;sul2
- Tmt_acquired
- dfrA12;dfrA17
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- spurious_resistance_hits
- tet(A).v1*?-0%;tet(A).v1?-63%
- ybtS
- 6
- ybtX
- 15
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 37
- irp1
- 44
- ybtU
- 32
- ybtT
- 1
- ybtE
- 4
- fyuA
- 26*
Analysis performed: 2024-04-30; Kleborate v2.3.2
Schemes and loci
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Tools
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