Full information on isolate SRR17308454 (id:39628)
Provenance/primary metadata
- id
- 39628
- isolate
- SRR17308454
- alias
- SAMN24297375
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 5 updates show details
- date entered
- 2023-02-15
- datestamp
- 2023-04-17
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2014
- city
- Unknown
- country
- UK
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Unknown
Sequence bin
- contigs
- 99
- total length
- 5,632,119 bp
- max length
- 316,544 bp
- mean length
- 56,891 bp
- N50
- 173,032
- L50
- 12
- N90
- 34,540
- L90
- 43
- N95
- 20,119
- L95
- 54
- %GC
- 56.98
- Ns
- 1050
- gaps
- 26
- loci tagged
- 685
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
rMLST species identification
Rank | Taxon | Taxonomy | Support | Matches |
---|---|---|---|---|
SPECIES | Klebsiella pneumoniae | Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2023-04-19
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 4
- resistance_score
- 2
- num_resistance_classes
- 8
- num_resistance_genes
- 12
- Yersiniabactin
- ybt 14; ICEKp5
- YbST
- 376
- CbST
- 0
- Aerobactin
- iuc 5
- AbST
- 61-3LV
- SmST
- 0
- RmST
- 0
- wzi
- wzi104
- K_locus
- KL51
- K_type
- K51
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 99.40%
- K_locus_missing_genes
- KL51_08_wcpB,KL51_14_wcoZ
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 98.44%
- O_locus_missing_genes
- O1/O2v2_06_wbbO
- AGly_acquired
- aadA2^;armA
- MLS_acquired
- ermB.v1*;mphA;mphE.v2;msrE
- Sul_acquired
- sul1
- Tmt_acquired
- dfrA12
- Bla_acquired
- CMY-4.v1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_Carb_acquired
- OXA-181
- Bla_chr
- SHV-1^
- Omp_mutations
- OmpK35-30%;OmpK36TD
- Flq_mutations
- GyrA-83I;ParC-80I
- ybtS
- 4
- ybtX
- 4
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 8
- irp1
- 8
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
- iucA
- 29
- iucB
- 17
- iucC
- 28
- iucD
- 35
- iutA
- 61
Analysis performed: 2024-04-12; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_88_0_0_0_0_1_6_0
Schemes and loci
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Tools
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