Full information on isolate GCA_004179405.1 (id:46784)
Projects
This isolate is a member of the following project:
- Hennart_et_al_2022_full_collection
- Collection of genomes from the paper "A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains" | PMID: 35700230
Provenance/primary metadata
- id
- 46784
- isolate
- GCA_004179405.1
- alias
- 071G9
- sender
- Mélanie Hennart, Institut Pasteur
- curator
- Auto Tagger
- update history
- 3 updates show details
- date entered
- 2023-03-23
- datestamp
- 2023-03-24
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- isolation year
- 0
- city
- Unknown
- country
- France
- continent
- Europe
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMN10840490
Sequence bin
- contigs
- 313
- total length
- 5,473,720 bp
- max length
- 147,689 bp
- mean length
- 17,488 bp
- N50
- 41,992
- L50
- 39
- N90
- 11,041
- L90
- 131
- N95
- 5,821
- L95
- 165
- %GC
- 57.41
- Ns
- 3741
- gaps
- 52
- loci tagged
- 702
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
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 1
- resistance_score
- 2
- num_resistance_classes
- 7
- num_resistance_genes
- 10
- Yersiniabactin
- ybt 9; ICEKp3
- YbST
- 157-1LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi173
- K_locus
- unknown (KL107)
- K_type
- unknown (KL107)
- K_locus_problems
- ?-+
- K_locus_confidence
- None
- K_locus_identity
- 87.85%
- K_locus_missing_genes
- KL107_05_wzb,KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10,KL107_12,KL107_13,KL107_14,KL107_15
- O_locus
- unknown (O1/O2v1)
- O_type
- unknown (O2a)
- O_locus_problems
- ?-
- O_locus_confidence
- None
- O_locus_identity
- 96.25%
- O_locus_missing_genes
- O1/O2v1_01_wzm,O1/O2v1_03_wbbM,O1/O2v1_04_glf,O1/O2v1_05_wbbN,O1/O2v1_06_wbbO,O1/O2v1_07_kfoC
- AGly_acquired
- aac(3)-IIa.v1^;aac(6')-Ib-cr.v2;strA.v1^;strB.v1
- Flq_acquired
- qnrB1.v2^
- Sul_acquired
- sul2
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_Carb_acquired
- OXA-48
- Bla_chr
- SHV-28.v1^
- Omp_mutations
- OmpK35-0%
- Flq_mutations
- GyrA-83I;ParC-80I
- truncated_resistance_hits
- CatB4.v1?-84%;OXA-1?-0%
- ybtS
- 41
- ybtX
- 11
- ybtQ
- 6
- ybtP
- 25
- ybtA
- 38
- irp2
- 255
- irp1
- 37
- ybtU
- 39
- ybtT
- 5
- ybtE
- 5
- fyuA
- 11
Analysis performed: 2024-04-17; Kleborate v2.3.2
Similar isolates (determined by classification schemes)
Experimental schemes are subject to change and are not a stable part of the nomenclature.
| Classification scheme | Underlying scheme | Clustering method | Mismatch threshold | Status | Group |
|---|---|---|---|---|---|
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 53 (481 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 55 (478 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 56 (291 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 58 (282 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 60 (272 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 61 (174 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 62 (113 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 62 (30 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 53 (481 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 55 (478 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 56 (291 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 58 (282 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 60 (272 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 61 (174 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 62 (113 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 62 (30 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: