TB-Profiler

TB-Profiler result

Run: dd2bbab1-4278-448c-8b2a-23023bfdcde4

This result has been migrated from an older version of TB-Profiler. Some information may be missing, and it has not been profiled using the latest mutation database. It is advised to re-run the analysis.

This average coverage of the target regions is below the recommended 30x. Some mutations may not be detected due to low coverage.

Summary

Run ID: dd2bbab1-4278-448c-8b2a-23023bfdcde4

Sample name:

Date: 02-04-2024 16:02:26

Number of reads: 966968

Percentage reads mapped: 98.51

Median coverage: 25

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs

Lineage	Family	RDs	Frequency
lineage2	East-Asian	RD105	1.0
lineage2.2	East-Asian (Beijing)	RD105;RD207	1.0
lineage2.2.1	East-Asian (Beijing)	RD105;RD207;RD181	1.0

Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes

Drug	Resistance	Supporting mutations	WHO confidence
rifampicin	rpoB	p.Ser450Leu	Assoc w R
isoniazid	fabG1	c.-15C>T	Assoc w R
isoniazid	katG	p.Ser315Thr	Assoc w R
ethambutol	embB	p.Gly406Ala	Assoc w R
pyrazinamide	pncA	p.Ile31Ser	Assoc w R
moxifloxacin	gyrA	p.Asp94Gly	Assoc w R
levofloxacin	gyrA	p.Asp94Gly	Assoc w R
bedaquiline
delamanid
pretomanid
linezolid
streptomycin	rpsL	p.Lys43Arg	Assoc w R
amikacin	rrs	n.1401A>G	Assoc w R
kanamycin	rrs	n.1401A>G	Assoc w R
capreomycin	rrs	n.1401A>G	Assoc w R
clofazimine
ethionamide	fabG1	c.-15C>T	Assoc w R
ethionamide	ethA	c.341delA	Assoc w R - interim
c.341delA	ethA	Uncertain significance
para-aminosalicylic_acid
cycloserine

Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence
gyrA	7582	p.Asp94Gly	missense_variant	1.0	ofloxacin	Uncertain significance
					moxifloxacin	Assoc w R
					levofloxacin	Assoc w R
					fluoroquinolones	Uncertain significance
					ciprofloxacin	Uncertain significance
rpoB	761155	p.Ser450Leu	missense_variant	1.0	rifampicin	Assoc w R
rpsL	781687	p.Lys43Arg	missense_variant	0.92	streptomycin	Assoc w R
rrs	1473246	n.1401A>G	non_coding_transcript_exon_variant	1.0	kanamycin	Assoc w R
					capreomycin	Assoc w R
					aminoglycosides	Uncertain significance
					amikacin	Assoc w R
fabG1	1673425	c.-15C>T	upstream_gene_variant	1.0	isoniazid	Assoc w R
fabG1	1673425	c.-15C>T	upstream_gene_variant	1.0	ethionamide	Assoc w R
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid	Assoc w R
pncA	2289150	p.Ile31Ser	missense_variant	1.0	pyrazinamide	Assoc w R
embB	4247730	p.Gly406Ala	missense_variant	1.0	ethambutol	Assoc w R
ethA	4327132	c.341delA	frameshift_variant	1.0	ethionamide	Assoc w R - interim
ethA	4327132	c.341delA	frameshift_variant	1.0	ethionamide	Uncertain significance

Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence
gyrA	7362	p.Glu21Gln	missense_variant	1.0	fluoroquinolones
					moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					ciprofloxacin
					ofloxacin
gyrA	7585	p.Ser95Thr	missense_variant	1.0	fluoroquinolones
					moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					ciprofloxacin
					ofloxacin
gyrA	9304	p.Gly668Asp	missense_variant	1.0	fluoroquinolones
					moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					ciprofloxacin
					ofloxacin
fgd1	491742	c.960T>C	synonymous_variant	1.0	delamanid
mshA	575907	p.Ala187Val	missense_variant	1.0	ethionamide	Uncertain significance
mshA	575907	p.Ala187Val	missense_variant	1.0	isoniazid	Uncertain significance
mshA	576751	p.Lys468Asn	missense_variant	0.27	ethionamide
mshA	576751	p.Lys468Asn	missense_variant	0.27	isoniazid
ccsA	620625	p.Ile245Met	missense_variant	1.0	capreomycin	Uncertain significance
ccsA	620625	p.Ile245Met	missense_variant	1.0	amikacin	Uncertain significance
rpoC	763031	c.-339T>C	upstream_gene_variant	1.0	rifampicin
rpoC	764715	p.Leu449Arg	missense_variant	0.91	rifampicin
rpoC	767084	p.Asn1239Asp	missense_variant	0.11	rifampicin	Uncertain significance
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Uncertain significance
mmpL5	775639	p.Ile948Val	missense_variant	1.0	bedaquiline	Uncertain significance
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	clofazimine	Uncertain significance
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	bedaquiline	Uncertain significance
mmpL5	776182	p.Asp767Asn	missense_variant	1.0	clofazimine	Uncertain significance
mmpL5	776182	p.Asp767Asn	missense_variant	1.0	bedaquiline	Uncertain significance
mmpL5	777119	p.His454Gln	missense_variant	0.16	clofazimine	Uncertain significance
mmpL5	777119	p.His454Gln	missense_variant	0.16	bedaquiline
mmpL5	777122	c.1359C>T	synonymous_variant	0.2	clofazimine
mmpL5	777122	c.1359C>T	synonymous_variant	0.2	bedaquiline
mmpL5	777128	c.1353A>G	synonymous_variant	0.21	clofazimine
mmpL5	777128	c.1353A>G	synonymous_variant	0.21	bedaquiline
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	clofazimine
mmpS5	779615	c.-710C>G	upstream_gene_variant	1.0	bedaquiline
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Uncertain significance
Rv1258c	1406760	c.580_581insC	frameshift_variant	1.0	streptomycin	Uncertain significance
					pyrazinamide	Uncertain significance
					isoniazid	Uncertain significance
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0	linezolid
					kanamycin
					capreomycin
					amikacin
					aminoglycosides
					streptomycin
fabG1	1673380	c.-60C>G	upstream_gene_variant	0.15	ethionamide
fabG1	1673380	c.-60C>G	upstream_gene_variant	0.15	isoniazid
inhA	1673709	c.-493C>T	upstream_gene_variant	1.0	ethionamide
inhA	1673709	c.-493C>T	upstream_gene_variant	1.0	isoniazid
rpsA	1834177	c.636A>C	synonymous_variant	1.0	pyrazinamide
rpsA	1834944	p.Ala468Asp	missense_variant	0.15	pyrazinamide
tlyA	1917972	c.33A>G	synonymous_variant	1.0	capreomycin
ndh	2101656	c.1386delC	frameshift_variant	0.11	ethionamide
ndh	2101656	c.1386delC	frameshift_variant	0.11	isoniazid
katG	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	Uncertain significance
PPE35	2167745	p.Thr956Arg	missense_variant	0.13	pyrazinamide
PPE35	2167865	c.2748G>C	synonymous_variant	0.13	pyrazinamide
PPE35	2167868	c.2745A>C	synonymous_variant	0.12	pyrazinamide
PPE35	2167926	p.Leu896Ser	missense_variant	1.0	pyrazinamide	Uncertain significance
PPE35	2168140	p.Ala825Thr	missense_variant	0.14	pyrazinamide
PPE35	2168143	p.Phe824Leu	missense_variant	0.14	pyrazinamide
PPE35	2168150	c.2463T>C	synonymous_variant	0.12	pyrazinamide
PPE35	2169281	c.1332T>G	synonymous_variant	0.1	pyrazinamide
PPE35	2169902	p.Leu237Phe	missense_variant	0.18	pyrazinamide
PPE35	2169910	p.Asn235Tyr	missense_variant	0.24	pyrazinamide
PPE35	2170157	p.Ala152Ser	missense_variant	0.12	pyrazinamide
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Uncertain significance
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Uncertain significance
pncA	2289692	c.-451C>T	upstream_gene_variant	0.11	pyrazinamide
kasA	2518039	c.-76C>T	upstream_gene_variant	0.11	isoniazid
kasA	2518150	c.36C>A	synonymous_variant	0.18	isoniazid
kasA	2518669	c.555C>T	synonymous_variant	0.13	isoniazid
folC	2747353	c.246C>T	synonymous_variant	0.12	para-aminosalicylic_acid
pepQ	2860043	p.Gly126Arg	missense_variant	0.1	clofazimine
pepQ	2860043	p.Gly126Arg	missense_variant	0.1	bedaquiline
ribD	2986827	c.-12G>A	upstream_gene_variant	1.0	para-aminosalicylic_acid
Rv2752c	3065126	p.Ser356Pro	missense_variant	0.98	rifampicin
Rv2752c	3065126	p.Ser356Pro	missense_variant	0.98	isoniazid
thyA	3074483	c.-12C>A	upstream_gene_variant	0.1	para-aminosalicylic_acid
ald	3086731	c.-89A>G	upstream_gene_variant	1.0	cycloserine
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
Rv3083	3448574	c.71_72insA	frameshift_variant	0.11	ethionamide
fprA	3473996	c.-11_-10insA	upstream_gene_variant	1.0	capreomycin
fprA	3473996	c.-11_-10insA	upstream_gene_variant	1.0	amikacin
fprA	3475208	p.Asp401Val	missense_variant	0.1	capreomycin
fprA	3475208	p.Asp401Val	missense_variant	0.1	amikacin
Rv3236c	3612813	p.Thr102Ala	missense_variant	1.0	pyrazinamide	Uncertain significance
alr	3841546	c.-126C>A	upstream_gene_variant	0.1	cycloserine
clpC1	4039645	p.His354Asp	missense_variant	0.17	pyrazinamide
clpC1	4039654	p.Thr351Ser	missense_variant	0.12	pyrazinamide
embA	4242643	c.-590C>T	upstream_gene_variant	1.0	ethambutol
embC	4243095	p.Gly1078Val	missense_variant	0.1	ethambutol
embA	4243099	c.-134G>C	upstream_gene_variant	0.1	ethambutol
embA	4243102	c.-131G>T	upstream_gene_variant	0.11	ethambutol
embC	4243103	p.Thr1081Pro	missense_variant	0.1	ethambutol
embC	4243106	p.Arg1082Ser	missense_variant	0.1	ethambutol
embA	4243346	c.114A>G	synonymous_variant	1.0	ethambutol
embA	4243460	c.228C>T	synonymous_variant	1.0	ethambutol
embA	4245373	p.Pro714Leu	missense_variant	0.1	ethambutol
whiB6	4338371	p.Thr51Pro	missense_variant	0.95	streptomycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
whiB6	4338595	c.-75delG	upstream_gene_variant	1.0	streptomycin	Uncertain significance
					capreomycin	Uncertain significance
					amikacin	Uncertain significance
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin
gid	4407927	p.Glu92Asp	missense_variant	1.0	streptomycin	Uncertain significance