TB-Profiler

TB-Profiler result

Run: ERR2516485

Summary

Run ID: ERR2516485

Sample name:

Date: 19-10-2023 23:46:25

Number of reads: 3946586

Percentage reads mapped: 99.67

Strain: lineage4.3.4.2;lineage4.1.2.1

Drug-resistance: Pre-XDR-TB

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

Drug	Resistance	Supporting mutations
Rifampicin	R	rpoB p.Gln432Pro (0.68), rpoB p.Ser450Leu (0.50), rpoC p.Leu527Val (0.47)
Isoniazid	R	katG p.Ser315Thr (1.00), ahpC c.-48G>A (0.58)
Ethambutol	R	embB p.Met306Ile (0.29), embB p.Met306Ile (0.71)
Pyrazinamide	R	pncA p.Leu182Ser (0.56), pncA p.Ile90Thr (0.36)
Streptomycin
Fluoroquinolones	R	gyrB p.Asn499Thr (0.59), gyrA p.Ala90Val (0.32), gyrA p.Asp94Gly (0.62)
Moxifloxacin	R	gyrB p.Asn499Thr (0.59), gyrA p.Ala90Val (0.32), gyrA p.Asp94Gly (0.62)
Ofloxacin	R	gyrB p.Asn499Thr (0.59), gyrA p.Ala90Val (0.32), gyrA p.Asp94Gly (0.62)
Levofloxacin	R	gyrB p.Asn499Thr (0.59), gyrA p.Ala90Val (0.32), gyrA p.Asp94Gly (0.62)
Ciprofloxacin	R	gyrB p.Asn499Thr (0.59), gyrA p.Ala90Val (0.32), gyrA p.Asp94Gly (0.62)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid

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

Lineage	Family	Main Spoligotype	RDs	Frequency
lineage4	Euro-American	LAM;T;S;X;H	None	1.0
lineage4.3	Euro-American (LAM)	mainly-LAM	None	0.45
lineage4.1	Euro-American	T;X;H	None	0.55
lineage4.1.2	Euro-American	T;H	None	0.57
lineage4.3.4	Euro-American (LAM)	LAM	RD174	0.42
lineage4.1.2.1	Euro-American (Haarlem)	T1;H1	RD182	0.55
lineage4.3.4.2	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174	0.43

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
gyrB	6735	p.Asn499Thr	missense_variant	0.59	ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA	7570	p.Ala90Val	missense_variant	0.32	ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA	7582	p.Asp94Gly	missense_variant	0.62	ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB	761101	p.Gln432Pro	missense_variant	0.68	rifampicin
rpoB	761155	p.Ser450Leu	missense_variant	0.5	rifampicin
rpoC	764948	p.Leu527Val	missense_variant	0.47	rifampicin
katG	2155168	p.Ser315Thr	missense_variant	1.0	isoniazid
pncA	2288697	p.Leu182Ser	missense_variant	0.56	pyrazinamide
pncA	2288973	p.Ile90Thr	missense_variant	0.36	pyrazinamide
ahpC	2726145	c.-48G>A	upstream_gene_variant	0.58	isoniazid
embB	4247431	p.Met306Ile	missense_variant	0.29	ethambutol
embB	4247431	p.Met306Ile	missense_variant	0.71	ethambutol

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
gyrB	6140	p.Val301Leu	missense_variant	0.44
gyrA	7362	p.Glu21Gln	missense_variant	1.0
gyrA	7585	p.Ser95Thr	missense_variant	1.0
gyrA	9304	p.Gly668Asp	missense_variant	1.0
fgd1	491591	p.Lys270Met	missense_variant	0.57
mshA	575679	p.Asn111Ser	missense_variant	0.59
rpoB	760115	c.309C>T	synonymous_variant	0.68
rpoC	764817	p.Val483Gly	missense_variant	0.63
rpoC	764995	c.1626C>G	synonymous_variant	0.45
rpoC	765150	p.Gly594Glu	missense_variant	0.61
mmpL5	775639	p.Ile948Val	missense_variant	1.0
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0
rrs	1471659	n.-187C>T	upstream_gene_variant	1.0
rpsA	1833469	c.-73G>T	upstream_gene_variant	0.52
tlyA	1917972	c.33A>G	synonymous_variant	1.0
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0
kasA	2518076	c.-39C>T	upstream_gene_variant	0.59
thyA	3073868	p.Thr202Ala	missense_variant	0.42
ald	3086788	c.-32T>C	upstream_gene_variant	1.0
fprA	3473996	c.-11_-10insA	upstream_gene_variant	1.0
Rv3236c	3612009	p.Ala370Thr	missense_variant	0.49
Rv3236c	3612846	p.Pro91Ser	missense_variant	0.48
alr	3840719	c.702A>G	synonymous_variant	0.43
clpC1	4038287	c.2418C>T	synonymous_variant	0.5
panD	4044181	p.Asp34Gly	missense_variant	0.51
embA	4242643	c.-590C>T	upstream_gene_variant	1.0
embC	4242803	p.Val981Leu	missense_variant	0.44
embB	4248004	p.Gln497His	missense_variant	0.47
ubiA	4269671	p.Val55Leu	missense_variant	0.47
ethA	4326182	p.Phe431Ser	missense_variant	0.58
ethA	4326705	p.Pro257Ala	missense_variant	0.38
whiB6	4338595	c.-75delG	upstream_gene_variant	0.55
gid	4407691	p.Val171Gly	missense_variant	0.54
gid	4407970	p.Pro78Leu	missense_variant	0.42
gid	4408156	p.Leu16Arg	missense_variant	0.45