Full information on isolate ERR971961 (id:58980)
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
- 58980
- isolate
- ERR971961
- 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
- 1998
- 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
- ERR971961
Sequence bin
- contigs
- 84
- total length
- 5,370,942 bp
- max length
- 579,604 bp
- mean length
- 63,940 bp
- N50
- 278,362
- L50
- 8
- N90
- 58,473
- L90
- 25
- N95
- 32,927
- L95
- 32
- %GC
- 57.32
- Ns
- 118
- gaps
- 77
- loci tagged
- 688
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 | 626 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 0
- num_resistance_classes
- 6
- num_resistance_genes
- 7
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi108
- K_locus
- unknown (KL118)
- K_type
- unknown (KL118)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 97.51%
- K_locus_missing_genes
- KL118_12_wcqP,KL118_13_wzx,KL118_14_wcuN,KL118_18_rmlA,KL118_19_rmlD
- O_locus
- OL101
- O_type
- unknown (OL101)
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 92.04%
- O_locus_missing_genes
- OL101_02_rfbA,OL101_03_rfbD,OL101_09_glycosylhydrolase
- AGly_acquired
- aadA2^
- MLS_acquired
- mphA
- Phe_acquired
- catII.2*
- Sul_acquired
- sul1;sul2
- Tet_acquired
- tet(D)
- Tmt_acquired
- dfrA12
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
Analysis performed: 2024-04-30; Kleborate v2.3.2
Schemes and loci
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Tools
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