Full information on isolate ERR311480 (id:27071)
Projects
This isolate is a member of the following project:
- Ellington et al. 2019
- Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center (https://doi.org/10.1186/s13059-019-1785-1)
Provenance/primary metadata
- id
- 27071
- isolate
- ERR311480
- alias
- SAMEA2053714
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 6 updates show details
- date entered
- 2023-02-15
- datestamp
- 2023-11-27
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 0
- city
- Unknown
- country
- UK
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Unknown
Sequence bin
- contigs
- 359
- total length
- 5,635,370 bp
- max length
- 937,929 bp
- mean length
- 15,698 bp
- N50
- 272,619
- L50
- 6
- N90
- 37,191
- L90
- 22
- N95
- 5,828
- L95
- 39
- %GC
- 57.15
- Ns
- 1611
- gaps
- 20
- loci tagged
- 693
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
- 0
- resistance_score
- 1
- num_resistance_classes
- 9
- num_resistance_genes
- 16
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi19
- K_locus
- KL19
- K_type
- K19
- K_locus_problems
- *
- K_locus_confidence
- High
- K_locus_identity
- 94.93%
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.48%
- AGly_acquired
- aac(3)-IId^;aadA16*;aph3-Ia.v1;strB.v1
- Flq_acquired
- qnrB4;qnrB6^
- MLS_acquired
- mphA
- Phe_acquired
- catB3.v2;catII.2*
- Rif_acquired
- arr-3
- Tet_acquired
- tet(A).v1
- Tmt_acquired
- dfrA27
- Bla_acquired
- DHA-1;OXA-1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-1^
- Omp_mutations
- OmpK35-18%
- Flq_mutations
- GyrA-83I;ParC-80I
- spurious_resistance_hits
- strA.v1?-0%;sul1?-52%;sul2?-0%
Analysis performed: 2024-03-26; Kleborate v2.3.2
Schemes and loci
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Tools
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