TB-Profiler

TB-Profiler result

Run: SRR13837688

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: SRR13837688

Sample name:

Date: 2024-10-05T10:19:17.481604

Number of reads: 294504

Percentage reads mapped: 98.23

Median coverage: 10.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide	ethA	p.Ser424*	Assoc w R
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
ethA	4326203	p.Ser424*	stop_gained	1.0	ethionamide	Assoc w R

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
dnaA	1057	p.Val353Leu	missense_variant	1.0	isoniazid	Uncertain significance
gyrB	5832	p.Ala198Gly	missense_variant	1.0	levofloxacin
gyrB	5832	p.Ala198Gly	missense_variant	1.0	moxifloxacin
gyrA	6976	c.-326A>G	upstream_gene_variant	1.0	levofloxacin
gyrA	6976	c.-326A>G	upstream_gene_variant	1.0	moxifloxacin
ccsA	619735	c.-156G>C	upstream_gene_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
tlyA	1918625	p.Pro229Leu	missense_variant	1.0	capreomycin
ndh	2103309	c.-267C>T	upstream_gene_variant	1.0	isoniazid
					delamanid
					ethionamide
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
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	1.0	pyrazinamide
embC	4241026	c.1164C>G	synonymous_variant	1.0	ethambutol
embB	4247398	c.885G>T	synonymous_variant	1.0	ethambutol
embB	4249328	p.Met939Leu	missense_variant	1.0	ethambutol