Full information on isolate D5478 (id:1844)

Provenance/primary metadata

id
1844
isolate
D5478
alias
SRR1999652
country
USA
continent
North America
region
Kansas
year
1998
disease
gastroenteritis
source
human stool
epidemiology
sporadic case
species
Campylobacter jejuni
penner
4
ENA run accession
SRR1999652 www.ebi.ac.uk
sender
Andrew Sails, CDC, Atlanta, USA
curator
Auto Tagger
update history
40 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
47
total length
1,727,327 bp
max length
303,553 bp
mean length
36,752 bp
N50
104,217
L50
5
N90
27,924
L90
19
N95
17,098
L95
23
%GC
30.33
Ns
0
gaps
0
loci tagged
1,643

Show sequence bin

Annotation quality metrics

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
MLST77100
Ribosomal MLST5353100
C. jejuni / C. coli cgMLST v1.01343132598

Analysis

rMLST species identification

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

Analysis performed: 2023-01-11

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-linkage200experimental43 (1896 isolates)
Cjc_cgc_100C. jejuni / C. coli cgMLST v1.0Single-linkage100experimental13 (58 isolates)
Cjc_cgc_50C. jejuni / C. coli cgMLST v1.0Single-linkage50experimental15 (47 isolates)
Cjc_cgc_25C. jejuni / C. coli cgMLST v1.0Single-linkage25experimental16 (8 isolates)
Cjc_cgc_10C. jejuni / C. coli cgMLST v1.0Single-linkage10experimental17 (4 isolates)
Cjc_cgc_5C. jejuni / C. coli cgMLST v1.0Single-linkage5experimental17 (2 isolates)
Cjc_cgc_200C. jejuni / C. coli cgMLST v1.0Single-linkage200experimental43 (1896 isolates)
Cjc_cgc_100C. jejuni / C. coli cgMLST v1.0Single-linkage100experimental13 (58 isolates)
Cjc_cgc_50C. jejuni / C. coli cgMLST v1.0Single-linkage50experimental15 (47 isolates)
Cjc_cgc_25C. jejuni / C. coli cgMLST v1.0Single-linkage25experimental16 (8 isolates)
Cjc_cgc_10C. jejuni / C. coli cgMLST v1.0Single-linkage10experimental17 (4 isolates)
Cjc_cgc_5C. jejuni / C. coli cgMLST v1.0Single-linkage5experimental17 (2 isolates)

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