TB-Profiler

TB-Profiler result

Run: SRR13837691

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: SRR13837691

Sample name:

Date: 2024-10-05T07:37:55.612182

Number of reads: 297896

Percentage reads mapped: 96.32

Median coverage: 10.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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

Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	1.0
lineage4.9	Euro-American (H37Rv-like)	None	1.0

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

Drug	Resistance	Supporting mutations	WHO confidence	Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid

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	Comment

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
gyrB	5832	p.Ala198Gly	missense_variant	1.0	levofloxacin
gyrB	5832	p.Ala198Gly	missense_variant	1.0	moxifloxacin
ccsA	619735	c.-156G>C	upstream_gene_variant	1.0	kanamycin
					capreomycin
					amikacin
ccsA	620100	c.210G>T	synonymous_variant	1.0	kanamycin
					capreomycin
					amikacin
rpoB	759609	c.-198C>A	upstream_gene_variant	1.0	rifampicin	Uncertain significance
rpoC	763050	c.-320C>T	upstream_gene_variant	1.0	rifampicin
mmpS5	778642	p.Trp88*	stop_gained	1.0	bedaquiline	Uncertain significance
mmpS5	778642	p.Trp88*	stop_gained	1.0	clofazimine	Uncertain significance
inhA	1674891	p.Trp230Cys	missense_variant	0.92	isoniazid
inhA	1674891	p.Trp230Cys	missense_variant	0.92	ethionamide
tlyA	1918625	p.Pro229Leu	missense_variant	1.0	capreomycin
ahpC	2726345	p.Phe51Leu	missense_variant	1.0	isoniazid
Rv2477c	2784427	c.-385T>C	upstream_gene_variant	1.0	kanamycin
					levofloxacin
					moxifloxacin
					streptomycin
					rifampicin
					ethambutol
					amikacin
Rv2752c	3066881	c.-690C>A	upstream_gene_variant	1.0	levofloxacin
					moxifloxacin
					isoniazid
					rifampicin
					ethambutol
Rv2752c	3067095	c.-904G>C	upstream_gene_variant	1.0	levofloxacin
					moxifloxacin
					isoniazid
					rifampicin
					ethambutol
whiB7	3568676	p.Ser2Ala	missense_variant	1.0	kanamycin	Uncertain significance
					amikacin	Uncertain significance
					streptomycin	Uncertain significance
alr	3840783	c.637_638insT	frameshift_variant	1.0	cycloserine
clpC1	4038326	p.Glu793Asp	missense_variant	0.94	pyrazinamide
panD	4044544	c.-263G>C	upstream_gene_variant	1.0	pyrazinamide
embC	4241026	c.1164C>G	synonymous_variant	1.0	ethambutol
aftB	4267490	c.1347G>C	synonymous_variant	1.0	ethambutol