TB-Profiler result

Run: ERR9786164
Summary

Run ID: ERR9786164

Sample name:

Date: 2024-04-14T14:45:50.209695

Number of reads: 683881

Percentage reads mapped: 55.85

Median coverage: 26.0

Strain: lineage4.1.1.3

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.1.3 Euro-American (X-type) RD193 1.0
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 1.0
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
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
cycloserine
ethionamide
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 0.42 rifampicin Assoc w R - Interim
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.5 amikacin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.27 amikacin Assoc w R
kanamycin Assoc w R
capreomycin 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 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760991 c.1185G>C synonymous_variant 0.3 rifampicin
rpoB 760997 c.1191G>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoB 761006 c.1200C>G synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoB 761013 c.1207_1209delGTGinsAC frameshift_variant&missense_variant 0.42 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoB 761046 c.1240_1242delATCinsGG frameshift_variant&missense_variant 0.48 rifampicin
rpoB 761051 c.1245G>C synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoB 761087 c.1281C>G synonymous_variant 0.52 rifampicin
rpoB 761088 c.1282_1284delAGCinsTCG synonymous_variant 0.52 rifampicin
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.48 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.45 rifampicin
rpoB 761126 c.1320G>C synonymous_variant 0.42 rifampicin
rpoB 761132 c.1326G>T synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 761162 c.1356G>C synonymous_variant 0.34 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoB 761171 c.1365C>T synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoB 761175 c.1371_1372delGT frameshift_variant 0.32 rifampicin
rpoB 761180 c.1374_1375insGC frameshift_variant 0.33 rifampicin
rpoB 761189 c.1383T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761196 c.1390_1392delCTGinsGC frameshift_variant&missense_variant 0.35 rifampicin
rpoB 761207 c.1401C>T synonymous_variant 0.35 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.33 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 762932 c.-438G>C upstream_gene_variant 0.23 rifampicin
rpoC 762947 c.-423C>G upstream_gene_variant 0.26 rifampicin
rpoB 762962 c.3156C>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 762980 c.-390T>C upstream_gene_variant 0.32 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.31 rifampicin
rpoB 762995 c.3189G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 763005 p.Cys1067Val missense_variant 0.3 rifampicin
rpoC 763013 c.-357C>G upstream_gene_variant 0.29 rifampicin
rpoB 763014 c.3208_3210delATGinsCC frameshift_variant&missense_variant 0.3 rifampicin
rpoB 763017 p.Gln1071Glu missense_variant 0.29 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.25 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 763038 c.3232_3234delACCinsGG frameshift_variant&missense_variant 0.25 rifampicin
rpoC 763052 c.-318G>C upstream_gene_variant 0.28 rifampicin
rpoB 763053 c.3247T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 763058 c.-312C>G upstream_gene_variant 0.29 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 763075 p.Thr1090Ile missense_variant 0.31 rifampicin
rpoB 763094 c.3288G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 763126 p.Pro1107Gln missense_variant 0.24 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763589 p.Ile74Val missense_variant 0.22 rifampicin
rpoC 763642 c.273G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764353 c.984G>C synonymous_variant 0.19 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764371 c.1002G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764381 c.1012_1013delTCinsAG synonymous_variant 0.21 rifampicin
rpoC 764387 c.1018T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.33 rifampicin
rpoC 764428 c.1059G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764431 c.1062G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764432 p.Lys355Arg missense_variant 0.35 rifampicin
rpoC 764435 c.1066_1068delAGGinsCC frameshift_variant&missense_variant 0.36 rifampicin
rpoC 764446 c.1077T>C synonymous_variant 0.37 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.37 rifampicin
rpoC 764455 c.1086G>C synonymous_variant 0.38 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764470 c.1101C>G synonymous_variant 0.46 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764498 p.Ser377Ala missense_variant 0.51 rifampicin
rpoC 764503 c.1134G>C synonymous_variant 0.53 rifampicin
rpoC 764509 c.1140G>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 764533 c.1164C>T synonymous_variant 0.52 rifampicin
rpoC 764536 c.1167G>T synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>T synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoC 764549 c.1180_1182delCCGinsAC frameshift_variant&missense_variant 0.52 rifampicin
rpoC 764561 p.Pro398Ala missense_variant 0.55 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.47 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.47 rifampicin
rpoC 764611 c.1242G>C synonymous_variant 0.45 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.39 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764660 c.1291_1293delGTGinsAC frameshift_variant&missense_variant 0.25 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764683 c.1314G>C synonymous_variant 0.23 rifampicin
rpoC 764692 c.1323C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764705 p.Leu446Ala missense_variant 0.16 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472256 n.411T>C non_coding_transcript_exon_variant 0.33 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472496 n.651T>G non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472507 n.662C>T non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472606 n.761C>G non_coding_transcript_exon_variant 0.39 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472645 n.800G>C non_coding_transcript_exon_variant 0.42 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>A non_coding_transcript_exon_variant 0.34 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472666 n.821G>T non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472686 n.841G>A non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472694 n.849C>A non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472993 n.1148G>T non_coding_transcript_exon_variant 0.34 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.51 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.51 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.52 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473134 n.1289T>C non_coding_transcript_exon_variant 0.54 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.59 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473269 n.1424C>T non_coding_transcript_exon_variant 0.42 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.33 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.36 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474466 n.809G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474488 n.831G>C non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>G non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.29 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 1474676 n.1019T>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1474723 n.1066G>A non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474770 n.1113G>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.26 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474800 n.1143T>C non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475768 n.2111_2112delGTinsC non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.31 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 0.32 capreomycin
linezolid Uncertain significance
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.4 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.4 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.4 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.38 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833742 c.201A>G synonymous_variant 0.24 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.24 pyrazinamide
rpsA 1833769 c.228C>G synonymous_variant 0.22 pyrazinamide
rpsA 1833781 c.240T>C synonymous_variant 0.24 pyrazinamide
rpsA 1833782 p.Ser81Lys missense_variant 0.24 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.26 pyrazinamide
rpsA 1833808 c.267G>C synonymous_variant 0.26 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.26 pyrazinamide
rpsA 1833815 p.Thr92Gln missense_variant 0.26 pyrazinamide
rpsA 1833829 c.288A>G synonymous_variant 0.29 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.29 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.32 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.38 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.35 pyrazinamide
rpsA 1833884 p.Thr115Asp missense_variant 0.33 pyrazinamide
rpsA 1833887 p.Ile116Val missense_variant 0.33 pyrazinamide
rpsA 1833893 p.Ala118Lys missense_variant 0.33 pyrazinamide
rpsA 1833896 p.Leu119Ile missense_variant 0.34 pyrazinamide
rpsA 1833907 p.Lys122Asn missense_variant 0.29 pyrazinamide
rpsA 1833912 p.Glu124Gly missense_variant 0.29 pyrazinamide
rpsA 1833915 p.Ala125Val missense_variant 0.29 pyrazinamide Uncertain significance
rpsA 1833921 p.Lys127Thr missense_variant 0.29 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.3 pyrazinamide
rpsA 1833955 c.414G>C synonymous_variant 0.2 pyrazinamide
rpsA 1833959 p.Leu140Val missense_variant 0.2 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833979 c.438T>G synonymous_variant 0.16 pyrazinamide
rpsA 1834423 c.882G>T synonymous_variant 0.3 pyrazinamide
rpsA 1834427 p.Ile296Val missense_variant 0.3 pyrazinamide Uncertain significance
rpsA 1834431 p.Val297Ala missense_variant 0.28 pyrazinamide Uncertain significance
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pepQ 2860619 c.-201C>T upstream_gene_variant 1.0 clofazimine
bedaquiline
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339178 p.Ala21Thr missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239763 c.-100C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin