TB-Profiler

Lineage	Family	RDs	Frequency
lineage2	East-Asian	RD105	0.43
lineage2.2.1	East-Asian (Beijing)	RD105;RD207;RD181	0.27
lineage2.2	East-Asian (Beijing)	RD105;RD207	1.0

Gene	Chromosome position	Mutation	Type	Estimated fraction	Drugs	Confidence	Comment
rpsL	781687	p.Lys43Arg	missense_variant	1.0	streptomycin	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
gyrA	9304	p.Gly668Asp	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	moxifloxacin	Not assoc w R
rpoB	762894	c.3088C>T	synonymous_variant	0.84	rifampicin	Not assoc w R - Interim
rpoB	762899	c.3093G>C	synonymous_variant	0.89	rifampicin	Not assoc w R - Interim
rpoB	762911	p.Ile1035Met	missense_variant	0.92	rifampicin
rpoB	762917	c.3111C>G	synonymous_variant	0.92	rifampicin	Not assoc w R - Interim
rpoB	762920	c.3114C>T	synonymous_variant	0.88	rifampicin	Not assoc w R - Interim
rpoB	762923	c.3117C>G	synonymous_variant	0.88	rifampicin	Not assoc w R - Interim
rpoB	762929	c.3123G>T	synonymous_variant	0.92	rifampicin	Not assoc w R - Interim
rpoB	762939	p.Met1045Leu	missense_variant	0.88	rifampicin
rpoB	762942	p.Ile1046Val	missense_variant	0.88	rifampicin	Uncertain significance
rpoC	762947	c.-423C>G	upstream_gene_variant	0.88	rifampicin
rpoC	762971	c.-399G>C	upstream_gene_variant	0.92	rifampicin
rpoB	762989	c.3183G>T	synonymous_variant	0.85	rifampicin	Not assoc w R - Interim
rpoC	764623	c.1254C>G	synonymous_variant	0.67	rifampicin	Not assoc w R - Interim
rpoC	764632	c.1263T>C	synonymous_variant	0.67	rifampicin	Not assoc w R - Interim
rpoC	764635	c.1266C>G	synonymous_variant	0.53	rifampicin
rpoC	764650	c.1281G>T	synonymous_variant	0.87	rifampicin	Not assoc w R - Interim
rpoC	764665	c.1296C>G	synonymous_variant	0.82	rifampicin
rpoC	764672	p.Gln435Thr	missense_variant	0.87	rifampicin
rpoC	764686	c.1317C>T	synonymous_variant	0.6	rifampicin
rpoC	764695	c.1326T>C	synonymous_variant	0.6	rifampicin
rpoC	764716	c.1347G>C	synonymous_variant	0.64	rifampicin	Not assoc w R - Interim
rpoC	764911	c.1542A>G	synonymous_variant	0.53	rifampicin
rpoC	764912	p.Met515Val	missense_variant	0.5	rifampicin
rpoC	764918	p.Val517Ile	missense_variant	0.56	rifampicin
rpoC	764935	c.1566T>C	synonymous_variant	0.62	rifampicin
mmpL5	776182	p.Asp767Asn	missense_variant	0.9	bedaquiline	Not assoc w R
mmpL5	776182	p.Asp767Asn	missense_variant	0.9	clofazimine	Not assoc w R
rrs	1472172	n.327T>C	non_coding_transcript_exon_variant	0.76	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472210	n.365A>T	non_coding_transcript_exon_variant	0.83	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472214	n.369C>G	non_coding_transcript_exon_variant	0.83	kanamycin
					capreomycin
					streptomycin	Uncertain significance
					amikacin
rrs	1472223	n.378C>G	non_coding_transcript_exon_variant	0.49	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472228	n.383G>C	non_coding_transcript_exon_variant	0.5	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472235	n.390G>C	non_coding_transcript_exon_variant	0.95	kanamycin
					capreomycin
					streptomycin	Uncertain significance
					amikacin
rrs	1472240	n.395G>A	non_coding_transcript_exon_variant	0.95	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472242	n.397C>T	non_coding_transcript_exon_variant	0.95	kanamycin
					capreomycin
					streptomycin	Uncertain significance
					amikacin
rrs	1472251	n.406G>C	non_coding_transcript_exon_variant	0.41	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472251	n.406G>T	non_coding_transcript_exon_variant	0.53	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472252	n.407G>A	non_coding_transcript_exon_variant	0.4	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472253	n.408G>T	non_coding_transcript_exon_variant	0.54	kanamycin
					capreomycin
					streptomycin	Uncertain significance
					amikacin
rrs	1472256	n.411T>A	non_coding_transcript_exon_variant	0.52	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472259	n.414C>A	non_coding_transcript_exon_variant	0.92	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472277	n.432C>G	non_coding_transcript_exon_variant	0.46	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472734	n.889C>T	non_coding_transcript_exon_variant	0.42	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472741	n.896G>A	non_coding_transcript_exon_variant	0.42	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472742	n.897C>T	non_coding_transcript_exon_variant	0.82	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472744	n.899A>G	non_coding_transcript_exon_variant	0.38	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472767	n.922G>A	non_coding_transcript_exon_variant	0.89	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1472781	n.936C>T	non_coding_transcript_exon_variant	0.83	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472785	n.940G>T	non_coding_transcript_exon_variant	0.8	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472786	n.941C>G	non_coding_transcript_exon_variant	0.8	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1472793	n.948A>T	non_coding_transcript_exon_variant	0.37	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1472814	n.969G>A	non_coding_transcript_exon_variant	0.82	kanamycin
					capreomycin
					streptomycin
					amikacin
rrs	1473147	n.1302G>T	non_coding_transcript_exon_variant	0.4	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473148	n.1303G>A	non_coding_transcript_exon_variant	0.39	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473163	n.1318C>T	non_coding_transcript_exon_variant	0.64	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473164	n.1319C>A	non_coding_transcript_exon_variant	0.62	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473172	n.1327T>C	non_coding_transcript_exon_variant	0.56	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1473173	n.1328C>T	non_coding_transcript_exon_variant	0.56	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Not assoc w R
					amikacin	Not assoc w R
rrs	1473177	n.1332G>A	non_coding_transcript_exon_variant	0.67	kanamycin	Uncertain significance
					capreomycin	Not assoc w R
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473192	n.1347A>G	non_coding_transcript_exon_variant	0.64	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Not assoc w R
rrs	1473201	n.1356_1357delACinsT	non_coding_transcript_exon_variant	0.62	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473205	n.1360T>C	non_coding_transcript_exon_variant	0.62	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrs	1473226	n.1381C>T	non_coding_transcript_exon_variant	0.77	kanamycin	Uncertain significance
					capreomycin	Uncertain significance
					streptomycin	Uncertain significance
					amikacin	Uncertain significance
rrl	1475803	n.2146T>C	non_coding_transcript_exon_variant	0.75	capreomycin	Uncertain significance
rrl	1475803	n.2146T>C	non_coding_transcript_exon_variant	0.75	linezolid	Uncertain significance
rrl	1475804	n.2147G>C	non_coding_transcript_exon_variant	0.82	capreomycin	Uncertain significance
rrl	1475804	n.2147G>C	non_coding_transcript_exon_variant	0.82	linezolid	Uncertain significance
rrl	1475816	n.2159C>G	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1475816	n.2159C>G	non_coding_transcript_exon_variant	0.8	linezolid	Uncertain significance
rrl	1475817	n.2160A>G	non_coding_transcript_exon_variant	0.8	capreomycin	Uncertain significance
rrl	1475817	n.2160A>G	non_coding_transcript_exon_variant	0.8	linezolid	Uncertain significance
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.91	capreomycin
rrl	1476336	n.2679C>T	non_coding_transcript_exon_variant	0.91	linezolid
rrl	1476338	n.2681C>T	non_coding_transcript_exon_variant	0.89	capreomycin	Uncertain significance
rrl	1476338	n.2681C>T	non_coding_transcript_exon_variant	0.89	linezolid	Uncertain significance
rrl	1476356	n.2699C>A	non_coding_transcript_exon_variant	0.9	capreomycin
rrl	1476356	n.2699C>A	non_coding_transcript_exon_variant	0.9	linezolid
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.91	capreomycin
rrl	1476357	n.2700T>C	non_coding_transcript_exon_variant	0.91	linezolid
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.91	capreomycin	Uncertain significance
rrl	1476358	n.2701T>C	non_coding_transcript_exon_variant	0.91	linezolid	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.92	capreomycin	Uncertain significance
rrl	1476359	n.2702C>G	non_coding_transcript_exon_variant	0.92	linezolid	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.92	capreomycin	Uncertain significance
rrl	1476369	n.2712C>T	non_coding_transcript_exon_variant	0.92	linezolid	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.92	capreomycin	Uncertain significance
rrl	1476381	n.2724G>C	non_coding_transcript_exon_variant	0.92	linezolid	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.92	capreomycin	Uncertain significance
rrl	1476382	n.2725A>G	non_coding_transcript_exon_variant	0.92	linezolid	Uncertain significance
rrl	1476383	n.2726T>G	non_coding_transcript_exon_variant	0.94	capreomycin
rrl	1476383	n.2726T>G	non_coding_transcript_exon_variant	0.94	linezolid
rrl	1476384	n.2727G>T	non_coding_transcript_exon_variant	0.94	capreomycin
rrl	1476384	n.2727G>T	non_coding_transcript_exon_variant	0.94	linezolid
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.91	capreomycin	Uncertain significance
rrl	1476408	n.2751G>A	non_coding_transcript_exon_variant	0.91	linezolid	Uncertain significance
rrl	1476411	n.2754G>T	non_coding_transcript_exon_variant	0.91	capreomycin
rrl	1476411	n.2754G>T	non_coding_transcript_exon_variant	0.91	linezolid
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.89	capreomycin	Uncertain significance
rrl	1476425	n.2768G>T	non_coding_transcript_exon_variant	0.89	linezolid	Uncertain significance
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.21	capreomycin	Not assoc w R
rrl	1476428	n.2771C>T	non_coding_transcript_exon_variant	0.21	linezolid	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.86	capreomycin	Uncertain significance
rrl	1476429	n.2772A>C	non_coding_transcript_exon_variant	0.86	linezolid	Uncertain significance
rrl	1476442	n.2785T>A	non_coding_transcript_exon_variant	0.83	capreomycin
rrl	1476442	n.2785T>A	non_coding_transcript_exon_variant	0.83	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	0.81	capreomycin
rrl	1476455	n.2798C>A	non_coding_transcript_exon_variant	0.81	linezolid
rrl	1476456	n.2799A>T	non_coding_transcript_exon_variant	0.81	capreomycin
rrl	1476456	n.2799A>T	non_coding_transcript_exon_variant	0.81	linezolid
rrl	1476463	n.2806C>A	non_coding_transcript_exon_variant	0.79	capreomycin
rrl	1476463	n.2806C>A	non_coding_transcript_exon_variant	0.79	linezolid
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.86	capreomycin	Not assoc w R
rrl	1476466	n.2809C>T	non_coding_transcript_exon_variant	0.86	linezolid	Uncertain significance
rrl	1476470	n.2813C>T	non_coding_transcript_exon_variant	0.79	capreomycin	Uncertain significance
rrl	1476470	n.2813C>T	non_coding_transcript_exon_variant	0.79	linezolid	Uncertain significance
rrl	1476483	n.2826G>A	non_coding_transcript_exon_variant	0.7	capreomycin
rrl	1476483	n.2826G>A	non_coding_transcript_exon_variant	0.7	linezolid
ald	3086739	c.-81G>A	upstream_gene_variant	1.0	cycloserine
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine

Drug	Resistance	Supporting mutations	WHO confidence
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin	rpsL	p.Lys43Arg	Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid

TB-Profiler result