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Summary

Run ID: SRR8692894

Sample name:

Date: 2024-10-04T18:26:54.168217

Number of reads: 1686361

Percentage reads mapped: 67.22

Median coverage: 40.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage	Family	RDs	Frequency
lineage4	Euro-American	None	0.99
lineage4.9	Euro-American (H37Rv-like)	None	1.0

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence	Comment
rplC	801268	p.Cys154Arg	missense_variant	0.96	linezolid	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
Rv1258c	1406686	p.Val219Ile	missense_variant	0.97	streptomycin
					pyrazinamide
					isoniazid
rrs	1472847	n.1002G>C	non_coding_transcript_exon_variant	0.38	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrs	1472848	n.1003T>G	non_coding_transcript_exon_variant	0.38	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472849	n.1004C>G	non_coding_transcript_exon_variant	0.38	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrs	1472850	n.1005T>C	non_coding_transcript_exon_variant	0.38	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472857	n.1012A>G	non_coding_transcript_exon_variant	0.4	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472858	n.1013G>T	non_coding_transcript_exon_variant	0.4	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472859	n.1014G>C	non_coding_transcript_exon_variant	0.4	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472860	n.1015C>G	non_coding_transcript_exon_variant	0.4	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin
					amikacin	Uncertain significance
rrl	1474753	n.1096A>G	non_coding_transcript_exon_variant	0.38	capreomycin	Uncertain significance
rrl	1474753	n.1096A>G	non_coding_transcript_exon_variant	0.38	linezolid
rrl	1474760	n.1103A>G	non_coding_transcript_exon_variant	0.35	capreomycin	Uncertain significance
rrl	1474760	n.1103A>G	non_coding_transcript_exon_variant	0.35	linezolid	Uncertain significance
rrl	1474794	n.1137C>T	non_coding_transcript_exon_variant	0.33	capreomycin	Uncertain significance
rrl	1474794	n.1137C>T	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1474812	n.1155G>A	non_coding_transcript_exon_variant	0.33	capreomycin	Uncertain significance
rrl	1474812	n.1155G>A	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1474830	n.1173A>G	non_coding_transcript_exon_variant	0.33	capreomycin	Uncertain significance
rrl	1474830	n.1173A>G	non_coding_transcript_exon_variant	0.33	linezolid	Uncertain significance
rrl	1475753	n.2096C>T	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1475753	n.2096C>T	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1475759	n.2102C>T	non_coding_transcript_exon_variant	0.8	capreomycin
rrl	1475759	n.2102C>T	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1475762	n.2105G>T	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1475762	n.2105G>T	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1475763	n.2106C>T	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1475763	n.2106C>T	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1475764	n.2107A>C	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1475764	n.2107A>C	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1475765	n.2108A>G	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1475765	n.2108A>G	non_coding_transcript_exon_variant	0.8	linezolid
rrl	1475775	n.2118G>A	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1475775	n.2118G>A	non_coding_transcript_exon_variant	0.82	linezolid
rrl	1476214	n.2557G>T	non_coding_transcript_exon_variant	0.38	capreomycin	Uncertain significance
rrl	1476214	n.2557G>T	non_coding_transcript_exon_variant	0.38	linezolid	Uncertain significance
rrl	1476215	n.2558C>T	non_coding_transcript_exon_variant	0.38	capreomycin	Uncertain significance
rrl	1476215	n.2558C>T	non_coding_transcript_exon_variant	0.38	linezolid	Uncertain significance
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.38	capreomycin	Uncertain significance
rrl	1476224	n.2567A>G	non_coding_transcript_exon_variant	0.38	linezolid	Uncertain significance
rrl	1476529	n.2872A>G	non_coding_transcript_exon_variant	0.37	capreomycin	Uncertain significance
rrl	1476529	n.2872A>G	non_coding_transcript_exon_variant	0.37	linezolid

Drug	Resistance	Supporting mutations	WHO confidence
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid	rplC	p.Cys154Arg	Assoc w R

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