TB-Profiler result

Run: ERR4407452
Summary

Run ID: ERR4407452

Sample name:

Date: 2024-10-05T08:33:27.476288

Number of reads: 1970041

Percentage reads mapped: 87.16

Median coverage: 89.0

Strain: lineage3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid ddn c.92delG Assoc w R - Interim Confers DLM-PMD cross-resistance
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
ddn 3986934 c.92delG frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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 8164 p.Ala288Asp missense_variant 0.93 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8294 c.993T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8324 c.1023T>C synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 8330 c.1029C>G synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8339 c.1038A>G synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 8340 p.Ala347Ser missense_variant 0.19 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8372 c.1071G>C synonymous_variant 0.21 levofloxacin
moxifloxacin
gyrA 8375 c.1074G>C synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 8382 p.Leu361Met missense_variant 0.18 levofloxacin
moxifloxacin
gyrA 8387 c.1086C>T synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8391 p.Tyr364His missense_variant 0.16 levofloxacin
moxifloxacin
gyrA 8399 c.1098T>G synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8401 p.Asp367Ala missense_variant 0.16 levofloxacin
moxifloxacin
gyrA 8405 c.1104C>T synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8420 c.1119T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8442 c.1141C>T synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8453 c.1152A>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8459 c.1158G>A synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8462 c.1161A>T synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8465 c.1164C>G synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8472 c.1171C>T synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8480 c.1179C>A synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8486 c.1185T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8504 c.1203G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8516 c.1215T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8519 c.1218A>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8520 c.1219C>T synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8528 c.1227G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8543 c.1242C>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8546 c.1245T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8552 c.1251C>A synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8807 c.1506C>T synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8828 c.1527T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8837 c.1536C>T synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8852 c.1551T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8858 c.1557T>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8867 c.1566A>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8870 c.1569G>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8873 c.1572A>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8891 c.1590G>A synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 8897 c.1596T>C synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8903 c.1602T>C synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8933 c.1632G>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8948 p.Leu549Phe missense_variant 0.16 levofloxacin
moxifloxacin
gyrA 8966 c.1665C>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8967 p.Ala556Arg missense_variant 0.16 levofloxacin
moxifloxacin
gyrA 8987 c.1686C>G synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8996 c.1695T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8998 p.Leu566Trp missense_variant 0.16 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin 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 657081 c.390G>A synonymous_variant 0.98 ethionamide Not assoc w R - Interim
hadA 732396 p.Gly156Ala missense_variant 0.14 isoniazid
hadA 732398 p.Ala157Thr missense_variant 0.14 isoniazid
rpoB 759746 c.-61C>T upstream_gene_variant 0.97 rifampicin Not assoc w R
rpoB 760472 c.666C>T synonymous_variant 0.14 rifampicin
rpoB 760991 c.1185G>C synonymous_variant 0.16 rifampicin
rpoB 761006 c.1200C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.15 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761102 c.1296A>G synonymous_variant 0.15 rifampicin
rpoB 761636 c.1830G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.15 rifampicin
rpoB 761657 c.1851C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761675 c.1869G>C synonymous_variant 0.16 rifampicin
rpoB 761720 c.1914C>G synonymous_variant 0.17 rifampicin
rpoB 761723 c.1917_1919delAGAinsC frameshift_variant&missense_variant 0.17 rifampicin
rpoB 761732 c.1926C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761735 c.1929C>G synonymous_variant 0.17 rifampicin
rpoB 761747 c.1941G>C synonymous_variant 0.18 rifampicin
rpoB 761750 c.1944G>C synonymous_variant 0.19 rifampicin
rpoB 761765 c.1959T>C synonymous_variant 0.18 rifampicin
rpoB 761772 p.His656Ala missense_variant 0.18 rifampicin
rpoB 761778 p.Asn658Asp missense_variant 0.18 rifampicin
rpoB 761791 p.Arg662His missense_variant 0.15 rifampicin
rpoB 761813 c.2007T>C synonymous_variant 0.15 rifampicin
rpoB 761815 p.Ala670Asp missense_variant 0.15 rifampicin
rpoB 762008 c.2202C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.16 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.15 rifampicin
rpoB 762140 c.2334G>C synonymous_variant 0.16 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.15 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762167 c.2361T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762206 c.2400C>G synonymous_variant 0.17 rifampicin
rpoB 762233 c.2427G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762246 c.2440C>T synonymous_variant 0.19 rifampicin
rpoB 762254 c.2448T>G synonymous_variant 0.19 rifampicin
rpoB 762257 c.2451C>G synonymous_variant 0.19 rifampicin
rpoB 762266 c.2460T>C synonymous_variant 0.18 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762293 c.2487T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762314 c.2508C>T synonymous_variant 0.16 rifampicin
rpoB 762317 c.2511A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 762989 c.-381G>C upstream_gene_variant 0.16 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.18 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763067 c.-303C>G upstream_gene_variant 0.23 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.15 rifampicin
rpoC 763657 c.288G>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.19 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.19 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.19 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.18 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.18 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.2 rifampicin
rpoC 763835 p.Ala156Met missense_variant 0.16 rifampicin
rpoC 763853 p.Val162Ile missense_variant 0.19 rifampicin
rpoC 763858 c.489A>G synonymous_variant 0.18 rifampicin
rpoC 763872 p.Gly168Ala missense_variant 0.18 rifampicin
rpoC 763876 p.Glu169Asp missense_variant 0.18 rifampicin
rpoC 763879 c.510A>G synonymous_variant 0.19 rifampicin
rpoC 763888 c.519G>C synonymous_variant 0.19 rifampicin
rpoC 763891 c.522G>C synonymous_variant 0.19 rifampicin
rpoC 763894 c.525A>G synonymous_variant 0.19 rifampicin
rpoC 763900 c.531G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763915 c.546C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763942 c.573C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763945 c.576T>C synonymous_variant 0.24 rifampicin
rpoC 763951 c.582G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763960 c.591T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763987 c.618C>T synonymous_variant 0.23 rifampicin
rpoC 763991 p.Ile208Leu missense_variant 0.22 rifampicin
rpoC 763996 c.627T>C synonymous_variant 0.22 rifampicin
rpoC 764002 c.633C>G synonymous_variant 0.23 rifampicin
rpoC 764005 c.636G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764020 c.651C>T synonymous_variant 0.21 rifampicin
rpoC 764024 c.655_657delTTGinsCTC synonymous_variant 0.21 rifampicin
rpoC 764032 p.Asp221Glu missense_variant 0.16 rifampicin
rpoC 764041 p.Ser224Arg missense_variant 0.16 rifampicin
rpoC 764044 c.675T>C synonymous_variant 0.17 rifampicin
rpoC 764059 c.690G>T synonymous_variant 0.14 rifampicin
rpoC 764353 c.984G>C synonymous_variant 0.14 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764381 p.Ser338Thr missense_variant 0.14 rifampicin
rpoC 764405 c.1036A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.15 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.15 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.16 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764489 c.1120C>T synonymous_variant 0.19 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765784 c.2415C>G synonymous_variant 0.15 rifampicin
rpoC 765787 c.2418C>T synonymous_variant 0.16 rifampicin
rpoC 765793 c.2424C>G synonymous_variant 0.16 rifampicin
rpoC 765796 c.2427C>T synonymous_variant 0.16 rifampicin
rpoC 765811 c.2442T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765850 c.2481G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765883 c.2514C>G synonymous_variant 0.14 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.15 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766795 c.3426C>T synonymous_variant 0.18 rifampicin
rpoC 766801 c.3432C>G synonymous_variant 0.18 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.21 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.25 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.26 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.25 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.22 rifampicin
rpoC 767014 c.3645G>C synonymous_variant 0.21 rifampicin
rpoC 767033 c.3664_3666delTCGinsAGC synonymous_variant 0.17 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.14 rifampicin
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
rpsL 781772 c.213C>A synonymous_variant 0.14 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.15 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.15 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.15 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.15 streptomycin
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 1303920 c.990C>T synonymous_variant 0.14 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474291 n.635_649delTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475267 n.1610G>A non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475589 n.1932G>A non_coding_transcript_exon_variant 0.76 capreomycin
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.34 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.18 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674624 c.423A>C synonymous_variant 0.14 isoniazid
ethionamide
rpsA 1833259 c.-283C>T upstream_gene_variant 1.0 pyrazinamide
rpsA 1834210 c.669C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834222 c.681T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.15 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834510 c.969C>T synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834513 c.972C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.17 pyrazinamide
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
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
ahpC 2726366 c.174G>C synonymous_variant 0.17 isoniazid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.94 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2477c 2782936 c.1107G>T synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783821 p.Gln74Leu missense_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783833 c.210G>C synonymous_variant 0.18 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyX 3067439 c.507A>G synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067442 c.504C>T synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067445 c.501C>G synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067457 c.489C>G synonymous_variant 0.14 para-aminosalicylic_acid
thyX 3067462 c.484C>T synonymous_variant 0.14 para-aminosalicylic_acid
thyX 3067510 c.436C>T synonymous_variant 0.14 para-aminosalicylic_acid
thyX 3067515 p.Ser144Thr missense_variant 0.14 para-aminosalicylic_acid
thyX 3067565 p.Asp127Glu missense_variant 0.14 para-aminosalicylic_acid
thyX 3067570 p.Ala126Pro missense_variant 0.15 para-aminosalicylic_acid
thyX 3067577 c.369G>A synonymous_variant 0.14 para-aminosalicylic_acid
thyX 3067602 p.Arg115Gln missense_variant 0.14 para-aminosalicylic_acid
thyX 3067631 c.315C>G synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067634 c.312C>G synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067637 c.309G>A synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067652 c.294T>C synonymous_variant 0.19 para-aminosalicylic_acid
thyX 3067661 c.285C>G synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067685 c.261A>C synonymous_variant 0.18 para-aminosalicylic_acid
thyX 3067691 p.Ile85Leu missense_variant 0.16 para-aminosalicylic_acid
thyX 3067694 c.252G>C synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067718 c.228C>G synonymous_variant 0.19 para-aminosalicylic_acid
thyX 3067721 c.225T>C synonymous_variant 0.19 para-aminosalicylic_acid
thyX 3067736 c.210C>T synonymous_variant 0.15 para-aminosalicylic_acid
thyX 3067762 c.184C>A synonymous_variant 0.13 para-aminosalicylic_acid
thyX 3067793 c.153T>C synonymous_variant 0.14 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3626969 c.381C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3626972 c.-359A>G upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3626987 c.-374C>G upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrB 3627008 c.-395G>C upstream_gene_variant 0.19 rifampicin
bedaquiline
mtrB 3627011 c.-398T>G upstream_gene_variant 0.2 rifampicin
bedaquiline
mtrB 3627065 c.-452G>C upstream_gene_variant 0.21 rifampicin
bedaquiline
mtrA 3627068 c.282T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
bedaquiline
mtrA 3627071 c.279G>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627074 c.-461G>C upstream_gene_variant 0.22 rifampicin
bedaquiline
mtrA 3627080 c.270T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627083 c.-470G>C upstream_gene_variant 0.2 rifampicin
bedaquiline
mtrA 3627098 c.252A>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627104 c.-491C>G upstream_gene_variant 0.23 rifampicin
bedaquiline
mtrA 3627119 c.231T>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627122 c.-509T>C upstream_gene_variant 0.21 rifampicin
bedaquiline
mtrA 3627146 c.204C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627167 c.-554T>C upstream_gene_variant 0.22 rifampicin
bedaquiline
mtrB 3627181 c.-568T>C upstream_gene_variant 0.21 rifampicin
bedaquiline
mtrB 3627182 c.-569T>C upstream_gene_variant 0.21 rifampicin
bedaquiline
mtrA 3627188 c.162A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627209 c.-596G>A upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrA 3627221 c.129C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
bedaquiline
mtrA 3627227 c.123T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627233 c.-620T>C upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3627236 c.-623T>C upstream_gene_variant 0.16 rifampicin
bedaquiline
mtrA 3627242 c.108C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627272 c.-659G>T upstream_gene_variant 0.13 rifampicin
bedaquiline
alr 3840482 c.939T>A synonymous_variant 1.0 cycloserine
alr 3841473 c.-53G>A upstream_gene_variant 1.0 cycloserine
rpoA 3878143 p.Gly122Asp missense_variant 0.14 rifampicin Uncertain significance
rpoA 3878163 c.345C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878169 c.339G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878172 c.336G>C synonymous_variant 0.16 rifampicin
rpoA 3878187 c.321C>G synonymous_variant 0.17 rifampicin
rpoA 3878193 c.315T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878199 c.309T>C synonymous_variant 0.19 rifampicin
rpoA 3878217 c.291A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878226 c.282C>G synonymous_variant 0.18 rifampicin
rpoA 3878232 c.276G>C synonymous_variant 0.18 rifampicin
rpoA 3878247 c.261G>C synonymous_variant 0.18 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878284 p.Glu75Ala missense_variant 0.17 rifampicin
rpoA 3878292 c.216T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878298 c.210A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>C synonymous_variant 0.17 rifampicin
rpoA 3878313 c.195G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878334 c.174T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.16 rifampicin
rpoA 3878364 c.144A>T synonymous_variant 0.15 rifampicin
rpoA 3878367 c.141C>G synonymous_variant 0.15 rifampicin
rpoA 3878376 c.132G>C synonymous_variant 0.19 rifampicin
rpoA 3878478 c.30C>G synonymous_variant 0.16 rifampicin
rpoA 3878484 c.24C>A synonymous_variant 0.14 rifampicin
rpoA 3878490 c.18C>A synonymous_variant 0.15 rifampicin
rpoA 3878496 c.12A>T synonymous_variant 0.2 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.15 rifampicin
rpoA 3879121 c.-614T>G upstream_gene_variant 0.19 rifampicin
rpoA 3879127 c.-620T>C upstream_gene_variant 0.18 rifampicin
rpoA 3879154 c.-647T>C upstream_gene_variant 0.22 rifampicin
rpoA 3879160 c.-653A>G upstream_gene_variant 0.21 rifampicin
rpoA 3879178 c.-671T>C upstream_gene_variant 0.2 rifampicin
rpoA 3879190 c.-683C>G upstream_gene_variant 0.2 rifampicin
ddn 3987095 c.252G>A synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clpC1 4038971 c.1734T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4038997 c.1708T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039022 c.1683A>G synonymous_variant 0.17 pyrazinamide
clpC1 4039064 c.1641C>T synonymous_variant 0.14 pyrazinamide
clpC1 4039274 c.1431G>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4039319 c.1386T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4039322 c.1383T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039337 p.Thr456Gln missense_variant 0.15 pyrazinamide
clpC1 4039349 c.1356C>T synonymous_variant 0.16 pyrazinamide
clpC1 4039352 c.1353C>G synonymous_variant 0.18 pyrazinamide
clpC1 4039364 c.1341C>G synonymous_variant 0.18 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.17 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.18 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.18 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.18 pyrazinamide Uncertain significance
clpC1 4039430 c.1275T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039442 c.1263A>G synonymous_variant 0.15 pyrazinamide
clpC1 4039538 c.1167C>T synonymous_variant 0.89 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4241318 p.Pro486Thr missense_variant 0.99 ethambutol Uncertain significance
embC 4241591 p.Leu577Val missense_variant 0.15 ethambutol
embC 4241611 c.1749G>C synonymous_variant 0.15 ethambutol
embC 4241614 c.1752A>C synonymous_variant 0.15 ethambutol
embC 4241626 c.1764T>C synonymous_variant 0.15 ethambutol
embC 4242075 p.Arg738Gln missense_variant 0.96 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.94 ethambutol Not assoc w R
embB 4247566 c.1053C>A synonymous_variant 0.13 ethambutol
embB 4248208 c.1695C>T synonymous_variant 0.14 ethambutol
embB 4248220 c.1707A>C synonymous_variant 0.15 ethambutol
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 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