TB-Profiler result

Run: ERR3324368
Summary

Run ID: ERR3324368

Sample name:

Date: 2024-10-04T17:42:31.411270

Number of reads: 719386

Percentage reads mapped: 74.16

Median coverage: 35.0

Strain: lineage1.1.2;lineage6.2.3

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.84
lineage6.2 West-Africa 2 RD702 0.13
lineage1.1 Indo-Oceanic RD239 0.85
lineage1 Indo-Oceanic RD239 0.88
lineage6.2.3 West-Africa 2 RD702 0.1
lineage6 West-Africa 2 RD702 0.13
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser441Ala Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
cycloserine
ethionamide ethA p.Gly413Asp Uncertain significance Mutation from literature
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
rpoB 761127 p.Ser441Ala missense_variant 0.21 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.29 amikacin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
ethA 4326236 p.Gly413Asp missense_variant 0.84 ethionamide Uncertain significance Mutation from literature
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 6112 p.Met291Ile missense_variant 0.81 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.82 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6446 p.Ala403Ser missense_variant 0.24 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8493 p.Leu398Phe missense_variant 0.26 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9143 c.1842T>C synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.81 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.26 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 656298 c.1173G>C synonymous_variant 0.19 ethionamide
Rv0565c 656432 p.Gly347Ser missense_variant 0.13 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.83 rifampicin Not assoc w R
rpoB 761084 c.1278C>A synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761088 c.1282_1284delAGCinsTCG synonymous_variant 0.2 rifampicin
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.19 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.19 rifampicin
rpoB 761126 c.1320G>C synonymous_variant 0.21 rifampicin
rpoB 761132 c.1326G>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762879 p.Met1025Leu missense_variant 0.17 rifampicin Uncertain significance
rpoB 762899 c.3093G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 762911 c.-459C>T upstream_gene_variant 0.21 rifampicin
rpoC 762917 c.-453C>A upstream_gene_variant 0.23 rifampicin
rpoB 762923 c.3117C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 762926 c.-444C>G upstream_gene_variant 0.29 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 762932 c.-438G>C upstream_gene_variant 0.22 rifampicin
rpoB 762959 c.3153G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 762971 c.-399G>C upstream_gene_variant 0.16 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.23 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763005 p.Cys1067Gly missense_variant 0.14 rifampicin Uncertain significance
rpoB 763006 p.Cys1067Phe missense_variant 0.15 rifampicin
rpoC 763013 c.-357C>G upstream_gene_variant 0.21 rifampicin
rpoB 763014 p.Met1070Leu missense_variant 0.21 rifampicin
rpoB 763017 p.Gln1071Glu missense_variant 0.21 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763034 c.-336C>A upstream_gene_variant 0.15 rifampicin
rpoB 763038 p.Thr1078Ala missense_variant 0.22 rifampicin
rpoB 763053 c.3247T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763058 c.-312C>G upstream_gene_variant 0.18 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763075 p.Thr1090Ile missense_variant 0.19 rifampicin
rpoC 763486 c.117T>G synonymous_variant 0.12 rifampicin
rpoC 763492 c.123G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763507 c.138G>C synonymous_variant 0.12 rifampicin
rpoC 763511 p.Cys48Gly missense_variant 0.14 rifampicin
rpoC 763517 p.Lys50Gln missense_variant 0.12 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763532 p.Thr55Ser missense_variant 0.12 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763550 p.Tyr61Ala missense_variant 0.12 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763589 p.Ile74Val missense_variant 0.12 rifampicin
rpoC 763609 c.240C>G synonymous_variant 0.11 rifampicin
rpoC 763614 c.246_251delGACCCG disruptive_inframe_deletion 0.12 rifampicin
rpoC 763622 p.Ala85Thr missense_variant 0.12 rifampicin Uncertain significance
rpoC 763630 c.261G>C synonymous_variant 0.12 rifampicin
rpoC 763642 c.273G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763884 p.Ala172Val missense_variant 0.9 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.92 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.86 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.82 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.16 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.79 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.83 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.21 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 0.11 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.11 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472293 n.448C>A non_coding_transcript_exon_variant 0.11 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472297 n.453_465delGTCCGGGTTCTCT non_coding_transcript_exon_variant 0.12 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472313 n.468delGinsAA non_coding_transcript_exon_variant 0.12 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.12 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.11 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.11 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472333 n.488G>A non_coding_transcript_exon_variant 0.11 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472507 n.662C>T non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472606 n.761C>G non_coding_transcript_exon_variant 0.28 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.26 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472645 n.800G>C non_coding_transcript_exon_variant 0.26 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>A non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472666 n.821G>T non_coding_transcript_exon_variant 0.23 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472686 n.841G>A non_coding_transcript_exon_variant 0.18 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472694 n.849C>A non_coding_transcript_exon_variant 0.25 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.25 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.2 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472993 n.1148G>T non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.37 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473134 n.1289T>C non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.41 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473269 n.1424C>T non_coding_transcript_exon_variant 0.26 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1474723 n.1066G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474770 n.1113G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474800 n.1143T>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475104 n.1447T>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475108 n.1451C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475111 n.1454G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475116 n.1459G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475119 n.1462C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475692 n.2035G>C non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid
rrl 1475758 n.2101_2102delACinsG non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1475768 n.2111_2112delGTinsC non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 0.42 capreomycin
linezolid Uncertain significance
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476025 n.2368G>A non_coding_transcript_exon_variant 0.39 capreomycin
linezolid Uncertain significance
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1476032 n.2375C>G non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476033 n.2376T>G non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476034 n.2377C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476045 n.2388G>A non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476046 n.2389G>C non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476047 n.2390G>C non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476076 n.2419A>G non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476079 n.2422G>A non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476080 n.2423T>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476081 n.2424A>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476082 n.2425T>C non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476087 n.2430C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1476104 n.2448delG non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.44 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.44 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.52 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.52 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.42 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.39 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1476544 n.2887T>A non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1476566 n.2909A>T non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476601 n.2944G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.26 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.6 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.56 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063121 c.1608A>T synonymous_variant 0.17 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.85 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.85 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.81 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086728 c.-92C>T upstream_gene_variant 0.28 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.18 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.92 ethionamide Uncertain significance
whiB7 3568507 p.Gln58Arg missense_variant 0.89 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612800 p.Val106Ala missense_variant 0.25 pyrazinamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.21 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640414 c.-129G>T upstream_gene_variant 0.15 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rpoA 3878986 c.-479G>A upstream_gene_variant 0.17 rifampicin
clpC1 4040517 p.Val63Ala missense_variant 0.74 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.89 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.92 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.32 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.92 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4248746 p.Gly745Ser missense_variant 0.85 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338441 p.Tyr27* stop_gained 0.9 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.88 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.9 streptomycin Not assoc w R
gid 4408148 p.Ala19Pro missense_variant 0.8 streptomycin Uncertain significance