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Full information on isolate SRR6816589 (id:912)

Projects

This isolate is a member of the following projects:

cgMLST set-up study: Isolates included in the cgMLST study (Guglielmini et al. J CLin Microbiol 2021 https://pubmed.ncbi.nlm.nih.gov/34524891/)
Hennart_diphtOscan_2023_OtherIsolates: Publicly-available genomes and isolates from the French NRC (2018-2021)
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: 912
isolate: SRR6816589
alias: CD19
species: C. diphtheriae
biovar: Gravis
isolation year: 2014
country: Australia
continent: Oceania
travel history: Not documented
host: Human
source: Respiratory
accession number: PRJNA436425
sender: Julien Guglielmini, Institut Pasteur, France
curator: Auto Tagger
update history: 8 updates show details
date entered: 2020-01-10
datestamp: 2025-07-17

Publications (2)

Guglielmini J, Hennart M, Badell E, Toubiana J, Criscuolo A, Brisse S (2021). Genomic Epidemiology and Strain Taxonomy of Corynebacterium diphtheriae. J Clin Microbiol 59:e0158121
Timms VJ, Nguyen T, Crighton T, Yuen M, Sintchenko V (2018). Genome-wide comparison of Corynebacterium diphtheriae isolates from Australia identifies differences in the Pan-genomes between respiratory and cutaneous strains. BMC Genomics 19:869

Sequence bin

method: Illumina
contigs: 37
total length: 2,370,418 bp
max length: 416,820 bp
mean length: 64,066 bp
N50: 176,632
L50: 4
N90: 46,292
L90: 14
N95: 30,012
L95: 17
%GC: 53.45
Ns: 0
gaps: 0
loci tagged: 1,306

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_19_4_1_6_0_0_0_0
Species: C. diphtheriae
Lineage: 0_0
Sublineage: SL32
Clonal group: ClG32
Genetic cluster: GC28

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Prefix	Threshold	Matching isolates
0_0_19_4_1_6	8	1
0_0_19_4_1_6_0	4	1
0_0_19_4_1_6_0_0	2	1
0_0_19_4_1_6_0_0_0	1	1
0_0_19_4_1_6_0_0_0_0	0	1
0	1220	2380
0_0	1035	2162
0_0_19	500	102
0_0_19_4	55	53
0_0_19_4_1	25	45
0_0_19_4_1_6	8	1
0_0_19_4_1_6_0	4	1
0_0_19_4_1_6_0_0	2	1
0_0_19_4_1_6_0_0_0	1	1
0_0_19_4_1_6_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	23 (30 isolates)	SL: 32
Genomic_cluster	cgMLST	Single-linkage	25	experimental	23 (17 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	23 (30 isolates)	SL: 32
Genomic_cluster	cgMLST	Single-linkage	25	experimental	23 (17 isolates)

Schemes and loci

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

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Tools

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