Full information on isolate D5476 (id:1818)

Provenance/primary metadata

id
1818
isolate
D5476
alias
SRR1993471
country
USA
continent
North America
region
Kansas
year
1998
disease
gastroenteritis
source
human stool
epidemiology
general outbreak
species
Campylobacter jejuni
penner
19
ENA run accession
SRR1993471 www.ebi.ac.uk
sender
Andrew Sails, CDC, Atlanta, USA
curator
Auto Tagger
update history
34 updates show details
date entered
2002-07-15
datestamp
2022-08-25

Publication (1)

  • Fitzgerald C, Helsel LO, Nicholson MA, Olsen SJ, Swerdlow DL, Flahart R, Sexton J, Fields PI (2001). Evaluation of methods for subtyping Campylobacter jejuni during an outbreak involving a food handler. J Clin Microbiol 39:2386-90

Sequence bin

contigs
35
total length
1,649,847 bp
max length
196,730 bp
mean length
47,139 bp
N50
147,050
L50
5
N90
45,928
L90
13
N95
22,233
L95
15
%GC
30.48
Ns
0
gaps
0
loci tagged
1,549

Show sequence bin

Annotation quality metrics

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
MLST77100
Ribosomal MLST5353100
C. jejuni / C. coli cgMLST v1.01343132998

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Campylobacter jejuni Pseudomonadota > Epsilonproteobacteria > Campylobacterales > Campylobacteraceae > Campylobacter > Campylobacter jejuni 100%

Analysis performed: 2023-02-05

Similar isolates (determined by classification schemes)

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Cjc_cgc_200C. jejuni / C. coli cgMLST v1.0Single-linkage200experimental8 (365 isolates)
Cjc_cgc_100C. jejuni / C. coli cgMLST v1.0Single-linkage100experimental9 (238 isolates)
Cjc_cgc_50C. jejuni / C. coli cgMLST v1.0Single-linkage50experimental10 (4 isolates)
Cjc_cgc_25C. jejuni / C. coli cgMLST v1.0Single-linkage25experimental11 (4 isolates)
Cjc_cgc_10C. jejuni / C. coli cgMLST v1.0Single-linkage10experimental12 (4 isolates)
Cjc_cgc_5C. jejuni / C. coli cgMLST v1.0Single-linkage5experimental12 (4 isolates)
Cjc_cgc_200C. jejuni / C. coli cgMLST v1.0Single-linkage200experimental8 (365 isolates)
Cjc_cgc_100C. jejuni / C. coli cgMLST v1.0Single-linkage100experimental9 (238 isolates)
Cjc_cgc_50C. jejuni / C. coli cgMLST v1.0Single-linkage50experimental10 (4 isolates)
Cjc_cgc_25C. jejuni / C. coli cgMLST v1.0Single-linkage25experimental11 (4 isolates)
Cjc_cgc_10C. jejuni / C. coli cgMLST v1.0Single-linkage10experimental12 (4 isolates)
Cjc_cgc_5C. jejuni / C. coli cgMLST v1.0Single-linkage5experimental12 (4 isolates)

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