Full information on isolate SRR10028390 (id:30068)

Provenance/primary metadata

id
30068
isolate
SRR10028390
alias
SAMN12212196
sender
Sebastien Bridel, Institut Pasteur, Paris, France
curator
Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
update history
7 updates show details
date entered
2023-02-15
datestamp
2024-06-03
taxonomic designation
K. pneumoniae
QC status
0000
isolation year
2016
city
Unknown
country
Switzerland
continent
Europe
source type
Human
host
Human
source details
Unknown

Sequence bin

contigs
157
total length
5,475,757 bp
max length
297,054 bp
mean length
34,878 bp
N50
78,452
L50
22
N90
18,693
L90
71
N95
13,015
L95
89
%GC
57.25
Ns
897
gaps
9
loci tagged
700

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Annotation quality metrics

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
MLST77100
Ribosomal MLST5353100
scgMLST629_S62962198

Analysis

Kleborate

species
Klebsiella pneumoniae
species_match
strong
QC_warnings
ambiguous_bases
virulence_score
4
resistance_score
2
num_resistance_classes
8
num_resistance_genes
9
Yersiniabactin
ybt 14; ICEKp5 (truncated)
YbST
376-1LV
CbST
0
Aerobactin
iuc 5
AbST
61-3LV
SmST
0
RmST
0
wzi
wzi104
K_locus
unknown (KL107)
K_type
unknown (KL107)
K_locus_problems
?-+
K_locus_confidence
None
K_locus_identity
84.05%
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
O1/O2v1
O_type
O1
O_locus_confidence
Good
O_locus_identity
98.03%
O_locus_missing_genes
O1/O2v1_03_wbbM,O1/O2v1_07_kfoC
AGly_acquired
aac(6')-Ib;aadA2^;rmtF
MLS_acquired
mphA
Rif_acquired
arr-2
Sul_acquired
sul1
Tmt_acquired
dfrA12
Bla_acquired
TEM-1D.v1^
Bla_Carb_acquired
OXA-232
Bla_chr
SHV-1^
Omp_mutations
OmpK35-30%;OmpK36TD
Flq_mutations
GyrA-83I;GyrA-87N;ParC-80I
truncated_resistance_hits
CTX-M-15?-0%
spurious_resistance_hits
catA1*?-0%
ybtS
4
ybtX
4
ybtQ
5
ybtP
4
ybtA
1
irp2
8
irp1
8*-55%
ybtU
2
ybtT
4
ybtE
4
fyuA
2
iucA
29
iucB
17
iucC
28
iucD
35
iutA
61

Analysis performed: 2024-04-05; Kleborate v2.3.2

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_88_0_0_0_0_8_1_0

Show all thresholds

PrefixThresholdMatching isolates
0_0_88_0_0_07463
0_0_88_0_0_0_04320
0_0_88_0_0_0_0_825
0_0_88_0_0_0_0_8_112
0_0_88_0_0_0_0_8_1_002
061038011
0_058538011
0_0_88190519
0_0_88_043509
0_0_88_0_010498
0_0_88_0_0_07463
0_0_88_0_0_0_04320
0_0_88_0_0_0_0_825
0_0_88_0_0_0_0_8_112
0_0_88_0_0_0_0_8_1_002

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Export:
Third party:
Analysis: