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Full information on isolate FRC1039 (id:1186)

Projects

This isolate is a member of the following projects:

Hennart_diphtOscan_2023_OtherIsolates: Publicly-available genomes and isolates from the French NRC (2018-2021)
French Guiana 2016-2021 study: Isolates included in the French Guiana 2016-2021 study (Gaillet et al., Emerg Inf Dis, 2024, https://pubmed.ncbi.nlm.nih.gov/39043387/)
DelgadoBlas_LINcodes_2025: Dataset of 1,665 isolates of C. diphtheriae, C. belfantii and C. rouxii used for the population structure analysis of C. diphtheriae sensu lato.

Provenance/primary metadata

id: 1186
isolate: FRC1039
species: C. diphtheriae
biovar: Gravis
tox gene PCR: Negative
isolation year: 2020
country: French Guiana
continent: South America
state or locality: French Guiana
travel history: Not documented
host: Human
source: Blood
infection or disease: Not documented
sender: Virginie Passet, Institut Pasteur, France
curator: Auto Tagger
update history: 14 updates show details
embargo history: show details
date entered: 2021-01-25
datestamp: 2025-07-17

Sequence bin

method: Unknown
contigs: 57
total length: 2,397,869 bp
max length: 365,911 bp
mean length: 42,068 bp
N50: 98,917
L50: 6
N90: 21,152
L90: 24
N95: 13,390
L95: 31
%GC: 53.44
Ns: 0
gaps: 0
loci tagged: 1,294

Show sequence bin

Assembly checks

Check	Status	Warn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Similar isolates (determined by LIN codes)

Scheme: cgMLST
LIN code: 0_0_40_2_0_3_0_0_0_0
Species: C. diphtheriae
Lineage: 0_0
Sublineage: SL128
Clonal group: ClG128
Genetic cluster: GC54

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Prefix	Threshold	Matching isolates
0_0_40_2_0_3	8	1
0_0_40_2_0_3_0	4	1
0_0_40_2_0_3_0_0	2	1
0_0_40_2_0_3_0_0_0	1	1
0_0_40_2_0_3_0_0_0_0	0	1
0	1220	2380
0_0	1035	2162
0_0_40	500	10
0_0_40_2	55	8
0_0_40_2_0	25	8
0_0_40_2_0_3	8	1
0_0_40_2_0_3_0	4	1
0_0_40_2_0_3_0_0	2	1
0_0_40_2_0_3_0_0_0	1	1
0_0_40_2_0_3_0_0_0_0	0	1

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	Fields
Sublineage	cgMLST	Single-linkage	500	experimental	17 (10 isolates)	SL: 128
Genomic_cluster	cgMLST	Single-linkage	25	experimental	341 (8 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	17 (10 isolates)	SL: 128
Genomic_cluster	cgMLST	Single-linkage	25	experimental	341 (8 isolates)

Schemes and loci

All loci
- Classical schemes
- Other schemes
  - PBP
  - spuA_island

Navigate and select schemes within tree to display allele designations

Tools

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