TB-Profiler

Summary

Run ID: SRR13861245

Sample name:

Date: 2024-04-15T10:14:43.740554

Number of reads: 252213

Percentage reads mapped: 12.62

Median coverage: 8.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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

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	5532	c.295dupG	frameshift_variant	1.0	levofloxacin	Uncertain significance
gyrB	5532	c.295dupG	frameshift_variant	1.0	moxifloxacin
ccsA	619735	c.-156G>C	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin
ccsA	620100	c.210G>T	synonymous_variant	1.0	capreomycin
					amikacin
					kanamycin
Rv1258c	1407009	p.Ala111Asp	missense_variant	1.0	streptomycin
					isoniazid
					pyrazinamide
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.67	capreomycin
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.67	linezolid
rrl	1476356	n.2699C>A	non_coding_transcript_exon_variant	0.73	capreomycin
rrl	1476356	n.2699C>A	non_coding_transcript_exon_variant	0.73	linezolid
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.73	capreomycin
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.73	linezolid
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.73	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.73	linezolid	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.73	capreomycin	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.73	linezolid	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.77	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.77	linezolid	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.79	capreomycin	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.79	linezolid	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.79	capreomycin	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.79	linezolid	Uncertain significance
rrl	1476383	n.2726T>G	non_coding_transcript_exon_variant	0.77	capreomycin
rrl	1476383	n.2726T>G	non_coding_transcript_exon_variant	0.77	linezolid
rrl	1476384	n.2727G>T	non_coding_transcript_exon_variant	0.79	capreomycin
rrl	1476384	n.2727G>T	non_coding_transcript_exon_variant	0.79	linezolid
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.84	capreomycin	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.84	linezolid	Uncertain significance
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.84	capreomycin
rrl	1476411	n.2754G>A	non_coding_transcript_exon_variant	0.84	linezolid
rrl	1476425	n.2768G>A	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1476425	n.2768G>A	non_coding_transcript_exon_variant	0.8	linezolid	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1476442	n.2785T>A	non_coding_transcript_exon_variant	0.82	capreomycin
rrl	1476442	n.2785T>A	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1476443	n.2786G>T	non_coding_transcript_exon_variant	0.82	capreomycin
rrl	1476443	n.2786G>T	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1476455	n.2798C>A	non_coding_transcript_exon_variant	0.76	capreomycin
rrl	1476455	n.2798C>A	non_coding_transcript_exon_variant	0.76	linezolid
rrl	1476456	n.2799A>T	non_coding_transcript_exon_variant	0.76	capreomycin
rrl	1476456	n.2799A>T	non_coding_transcript_exon_variant	0.76	linezolid
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.77	capreomycin
rrl	1476463	n.2806C>T	non_coding_transcript_exon_variant	0.77	linezolid
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.75	capreomycin	Not assoc w R
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.75	linezolid	Uncertain significance
inhA	1674891	p.Trp230Cys	missense_variant	1.0	ethionamide
inhA	1674891	p.Trp230Cys	missense_variant	1.0	isoniazid
Rv1979c	2222721	c.444G>C	synonymous_variant	1.0	clofazimine
Rv1979c	2222721	c.444G>C	synonymous_variant	1.0	bedaquiline
ahpC	2726345	p.Phe51Leu	missense_variant	1.0	isoniazid
Rv2477c	2783258	c.784delC	frameshift_variant	1.0	ethambutol	Uncertain significance
					moxifloxacin	Uncertain significance
					streptomycin	Uncertain significance
					levofloxacin	Uncertain significance
					kanamycin	Uncertain significance
					rifampicin	Uncertain significance
					amikacin	Uncertain significance
whiB7	3568676	p.Ser2Ala	missense_variant	1.0	streptomycin	Uncertain significance
					amikacin	Uncertain significance
					kanamycin	Uncertain significance
glpK	4138911	p.Gly282Val	missense_variant	1.0	ethambutol
					moxifloxacin
					streptomycin
					levofloxacin
					rifampicin
					isoniazid
embA	4242250	c.-983C>G	upstream_gene_variant	1.0	ethambutol
embB	4249328	p.Met939Leu	missense_variant	1.0	ethambutol

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