Full information on isolate I_UW12 (id:4864)

Provenance/primary metadata

id
4864
isolate
I_UW12
species
Chlamydia trachomatis
genovar
I-Ia
country
USA
continent
North America
year
1966
host
human
source
urethra
bioproject accession
PRJEB2035 www.ebi.ac.uk
biosample accession
SAMEA1903274 www.ebi.ac.uk
ENA run accession
ERR278215 www.ebi.ac.uk
sender
Odile Harrison, University of Oxford, UK
curator
Auto Tagger
update history
6 updates show details
date entered
2022-07-08
datestamp
2022-12-01

Publication (1)

  • Hadfield J, Harris SR, Seth-Smith HMB, Parmar S, Andersson P, Giffard PM, Schachter J, Moncada J, Ellison L, Vaulet MLG, Fermepin MR, Radebe F, Mendoza S, Ouburg S, MorrĂ© SA, Sachse K, Puolakkainen M, Korhonen SJ, Sonnex C, Wiggins R, Jalal H, Brunelli T, Casprini P, Pitt R, Ison C, Savicheva A, Shipitsyna E, Hadad R, Kari L, Burton MJ, Mabey D, Solomon AW, Lewis D, Marsh P, Unemo M, Clarke IN, Parkhill J, Thomson NR (2017). Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion. Genome Res 27:1220-1229

Sequence bin

contigs
142
total length
1,791,476 bp
max length
562,665 bp
mean length
12,617 bp
N50
204,861
L50
3
N90
11,877
L90
26
N95
5,855
L95
37
%GC
34.95
Ns
0
gaps
0
loci tagged
1,030

Show sequence bin

Annotation quality metrics

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
C. trachomatis cgMLST v1.081781499

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Chlamydia trachomatis Chlamydiae > Chlamydiia > Chlamydiales > Chlamydiaceae > Chlamydia > Chlamydia trachomatis 87%
SPECIES Metamycoplasma orale Tenericutes > [unclassified] > Mycoplasmoidales > Metamycoplasmataceae > Metamycoplasma > Metamycoplasma orale 10%

Analysis performed: 2023-01-25

Similar isolates (determined by classification schemes)

Some groups only contain this isolate. Show single groups

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

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Ct_cgc_200C. trachomatis cgMLST v1.0Single-linkage200experimental6 (99 isolates)
Ct_cgc_200C. trachomatis cgMLST v1.0Single-linkage200experimental6 (99 isolates)
Ct_cgc_100C. trachomatis cgMLST v1.0Single-linkage100experimental70 (1 isolate)
Ct_cgc_50C. trachomatis cgMLST v1.0Single-linkage50experimental123 (1 isolate)
Ct_cgc_25C. trachomatis cgMLST v1.0Single-linkage25experimental211 (1 isolate)
Ct_cgc_10C. trachomatis cgMLST v1.0Single-linkage10experimental278 (1 isolate)
Ct_cgc_5C. trachomatis cgMLST v1.0Single-linkage5experimental305 (1 isolate)

Schemes and loci

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Tools

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