TB-Profiler result

Run: ERR11465509
Summary

Run ID: ERR11465509

Sample name:

Date: 2024-10-04T02:54:47.039128

Number of reads: 742172

Percentage reads mapped: 84.13

Median coverage: 18.0

Strain: lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.96
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 0.92
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
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
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
dnaA 1104 c.1104T>C synonymous_variant 0.15 isoniazid
dnaA 1110 c.1110T>C synonymous_variant 0.15 isoniazid
dnaA 1113 c.1113A>G synonymous_variant 0.15 isoniazid
dnaA 1119 c.1119G>A synonymous_variant 0.21 isoniazid
dnaA 1122 c.1122C>G synonymous_variant 0.22 isoniazid
gyrB 5611 c.372C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6140 p.Val301Leu missense_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 6598 c.-704C>G upstream_gene_variant 0.35 levofloxacin
moxifloxacin
gyrA 6610 c.-692C>G upstream_gene_variant 0.33 levofloxacin
moxifloxacin
gyrA 6613 c.-689A>G upstream_gene_variant 0.33 levofloxacin
moxifloxacin
gyrA 6616 c.-686A>G upstream_gene_variant 0.33 levofloxacin
moxifloxacin
gyrB 6808 c.1569C>G synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6811 c.1572C>T synonymous_variant 0.23 levofloxacin
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7415 c.114C>G synonymous_variant 0.37 levofloxacin
moxifloxacin
gyrA 7418 c.117C>T synonymous_variant 0.39 levofloxacin
moxifloxacin
gyrA 7565 c.264C>G synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 7569 p.Ala90Ser missense_variant 0.23 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7592 c.291G>C synonymous_variant 0.38 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7601 c.300C>G synonymous_variant 0.36 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7607 c.306C>G synonymous_variant 0.36 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7626 c.325C>T synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 7631 c.330G>C synonymous_variant 0.3 levofloxacin
moxifloxacin
gyrA 7637 c.336C>G synonymous_variant 0.33 levofloxacin
moxifloxacin
gyrA 8294 c.993T>C synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8324 c.1023T>C synonymous_variant 0.34 levofloxacin
moxifloxacin
gyrA 8327 c.1026C>G synonymous_variant 0.34 levofloxacin
moxifloxacin
gyrA 8339 c.1038A>G synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 8340 p.Ala347Ser missense_variant 0.34 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8546 c.1245T>C synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8552 c.1251C>G synonymous_variant 0.28 levofloxacin
moxifloxacin
gyrA 8555 c.1254G>T synonymous_variant 0.29 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 8561 c.1260A>C synonymous_variant 0.32 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8619 c.1318T>C synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8636 c.1335A>C synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8829 c.1528T>C synonymous_variant 0.32 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8882 c.1581G>A synonymous_variant 0.37 levofloxacin
moxifloxacin
gyrA 8897 c.1596T>C synonymous_variant 0.29 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8900 c.1599G>C synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 8903 c.1602T>C synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8915 c.1614A>G synonymous_variant 0.28 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8967 p.Ala556Asn missense_variant 0.23 levofloxacin
moxifloxacin
gyrA 8996 c.1695T>C synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 8998 p.Leu566Trp missense_variant 0.24 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9023 c.1722A>C synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9029 c.1728T>G synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 9032 c.1731T>C synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 9038 c.1737C>G synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 9050 p.Asp583Glu missense_variant 0.19 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9056 c.1755C>G synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9062 c.1761C>G synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 9068 c.1767G>C synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 9080 c.1779G>T synonymous_variant 0.22 levofloxacin
moxifloxacin
ccsA 620604 c.714C>G synonymous_variant 0.43 kanamycin
capreomycin
amikacin
ccsA 620607 c.717T>G synonymous_variant 0.43 kanamycin
capreomycin
amikacin
ccsA 620613 c.723C>G synonymous_variant 0.43 kanamycin
capreomycin
amikacin
ccsA 620619 c.729G>C synonymous_variant 0.43 kanamycin
capreomycin
amikacin
ccsA 620625 c.735A>C synonymous_variant 0.46 kanamycin
capreomycin
amikacin
ccsA 620631 c.741T>C synonymous_variant 0.46 kanamycin
capreomycin
amikacin
ccsA 620634 c.744C>A synonymous_variant 0.5 kanamycin
capreomycin
amikacin
ccsA 620649 c.759A>G synonymous_variant 0.39 kanamycin
capreomycin
amikacin
ccsA 620652 c.762C>G synonymous_variant 0.39 kanamycin
capreomycin
amikacin
ccsA 620698 p.Val270Ile missense_variant 0.5 kanamycin
capreomycin
amikacin
rpoB 760283 c.477G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760310 c.504G>C synonymous_variant 0.17 rifampicin
rpoB 760508 c.702G>C synonymous_variant 0.33 rifampicin
rpoB 760511 c.705G>C synonymous_variant 0.29 rifampicin
rpoB 760522 p.Ser239Asn missense_variant 0.29 rifampicin Uncertain significance
rpoB 760591 p.Val262Ala missense_variant 0.22 rifampicin
rpoB 760611 c.805_807delTTGinsCTC synonymous_variant 0.26 rifampicin
rpoB 760670 c.864G>C synonymous_variant 0.17 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761318 c.1512G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 761327 c.1521A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761570 c.1764T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 762083 c.2277T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763028 c.3222T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.16 rifampicin Not assoc w R
rpoB 763040 c.3234C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763058 c.-312C>G upstream_gene_variant 0.31 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 763082 c.-288C>G upstream_gene_variant 0.41 rifampicin
rpoC 763103 c.-267G>C upstream_gene_variant 0.42 rifampicin
rpoB 763115 c.3309T>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 763127 c.3321G>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 763142 c.-228C>G upstream_gene_variant 0.29 rifampicin
rpoC 763160 c.-210G>T upstream_gene_variant 0.47 rifampicin
rpoB 763166 c.3360A>G synonymous_variant 0.51 rifampicin Not assoc w R - Interim
rpoC 763217 c.-153G>C upstream_gene_variant 0.32 rifampicin
rpoC 764131 c.762T>C synonymous_variant 0.24 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764800 c.1431G>A synonymous_variant 0.22 rifampicin
rpoC 764803 c.1434C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 764812 c.1443C>G synonymous_variant 0.16 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764857 c.1488G>T synonymous_variant 0.19 rifampicin
rpoC 764858 c.1489T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764878 c.1509C>G synonymous_variant 0.17 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 0.96 rifampicin Not assoc w R
rpoC 765493 c.2124G>C synonymous_variant 0.41 rifampicin
rpoC 765499 c.2130C>A synonymous_variant 0.41 rifampicin
rpoC 766423 c.3054T>C synonymous_variant 0.37 rifampicin
rpoC 766426 c.3057C>T synonymous_variant 0.37 rifampicin
rpoC 766429 c.3060C>G synonymous_variant 0.37 rifampicin
rpoC 766447 c.3078T>C synonymous_variant 0.5 rifampicin
rpoC 766459 c.3090G>C synonymous_variant 0.46 rifampicin
rpoC 766471 c.3102G>C synonymous_variant 0.5 rifampicin
rpoC 766483 c.3114G>C synonymous_variant 0.44 rifampicin
rpoC 766486 c.3117A>G synonymous_variant 0.44 rifampicin
rpoC 766492 c.3123T>G synonymous_variant 0.44 rifampicin
rpoC 766493 p.Gly1042Asn missense_variant 0.44 rifampicin
rpoC 766618 c.3249G>T synonymous_variant 0.23 rifampicin
rpoC 766624 c.3255G>C synonymous_variant 0.23 rifampicin
rpoC 766630 c.3261G>T synonymous_variant 0.23 rifampicin
rpoC 766634 p.Phe1089Ile missense_variant 0.23 rifampicin
rpoC 766645 c.3276A>G synonymous_variant 0.23 rifampicin
rpoC 766651 c.3282T>C synonymous_variant 0.21 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.3 rifampicin
rpoC 766690 c.3321G>C synonymous_variant 0.33 rifampicin
rpoC 766694 p.Gln1109Asp missense_variant 0.33 rifampicin
rpoC 766702 c.3333G>C synonymous_variant 0.38 rifampicin
rpoC 767023 c.3654C>T synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 767180 p.Ala1271Gln missense_variant 0.18 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767197 c.3828G>A synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 767221 c.3852C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 767230 c.3861G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 767233 c.3864T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775943 c.2538C>G synonymous_variant 0.24 bedaquiline
clofazimine
mmpL5 775951 c.2530C>T synonymous_variant 0.39 bedaquiline
clofazimine
mmpL5 775964 p.Ala839Ser missense_variant 0.26 bedaquiline
clofazimine
mmpL5 775975 p.Leu836Met missense_variant 0.35 bedaquiline
clofazimine
mmpL5 776681 c.1800G>C synonymous_variant 0.18 bedaquiline
clofazimine
mmpL5 776682 c.1798_1799insGA frameshift_variant 0.18 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776686 c.1793_1794delGG frameshift_variant 0.16 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776704 p.Asp593Asn missense_variant 0.17 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781841 c.282C>T synonymous_variant 0.19 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.17 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.17 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.18 streptomycin
rpsL 781880 c.321C>G synonymous_variant 0.16 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.24 streptomycin Uncertain significance
rplC 800594 c.-215C>G upstream_gene_variant 0.29 linezolid
rplC 800597 c.-212A>G upstream_gene_variant 0.29 linezolid
rplC 800600 c.-209G>C upstream_gene_variant 0.29 linezolid
rplC 800603 c.-206G>C upstream_gene_variant 0.36 linezolid
rplC 800612 c.-197A>G upstream_gene_variant 0.28 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.33 linezolid
rplC 800633 c.-176T>C upstream_gene_variant 0.29 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.31 linezolid
rplC 800672 c.-137G>T upstream_gene_variant 0.39 linezolid
rplC 800690 c.-119C>T upstream_gene_variant 0.32 linezolid
rplC 800693 c.-116A>T upstream_gene_variant 0.3 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.23 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.26 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.28 linezolid
rplC 800738 c.-71T>C upstream_gene_variant 0.24 linezolid
atpE 1461254 c.210T>C synonymous_variant 0.17 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1474287 n.630_635delTCCTTTinsCTCGACTTG non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1474294 n.638_649delCTCTCCGGAGGA non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474374 n.717T>G non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474708 n.1052_1053insACAAG non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1474711 n.1055_1058delGTGT non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1474720 n.1063C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475479 n.1822_1823delCAinsTG non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.38 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475989 n.2332T>A non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1476032 n.2375C>G non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476033 n.2376T>G non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1476046 n.2389G>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476088 n.2431A>T non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833772 c.231C>T synonymous_variant 0.3 pyrazinamide
rpsA 1833778 c.237C>T synonymous_variant 0.33 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.27 pyrazinamide
rpsA 1833991 c.450C>A synonymous_variant 0.32 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid 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 2517974 c.-141T>C upstream_gene_variant 0.18 isoniazid
kasA 2519203 c.1089C>T synonymous_variant 0.26 isoniazid
kasA 2519224 c.1110C>A synonymous_variant 0.32 isoniazid
Rv2477c 2782453 c.1590C>T synonymous_variant 0.39 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782465 c.1578G>A synonymous_variant 0.29 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782480 c.1563G>A synonymous_variant 0.2 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782486 c.1557G>A synonymous_variant 0.32 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyX 3067646 c.300C>G synonymous_variant 0.25 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624710 c.201G>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626773 c.-160C>T upstream_gene_variant 0.35 rifampicin
bedaquiline
mtrB 3626774 c.-163_-161delAGGinsCGT upstream_gene_variant 0.35 rifampicin
bedaquiline
mtrB 3626780 c.-167T>C upstream_gene_variant 0.3 rifampicin
bedaquiline
mtrB 3626783 c.-170C>G upstream_gene_variant 0.32 rifampicin
bedaquiline
mtrB 3626786 c.-173A>C upstream_gene_variant 0.35 rifampicin
bedaquiline
mtrA 3626792 c.558G>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
bedaquiline
mtrA 3626804 c.546A>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
bedaquiline
mtrA 3626825 c.525T>A synonymous_variant 0.38 rifampicin Not assoc w R - Interim
bedaquiline
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
rpoA 3877695 c.813C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoA 3877856 c.652T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoA 3877875 c.633T>G synonymous_variant 0.35 rifampicin
rpoA 3877881 c.627G>C synonymous_variant 0.42 rifampicin
rpoA 3877884 c.624G>C synonymous_variant 0.42 rifampicin
rpoA 3877893 c.615C>T synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoA 3877900 p.Ser203Thr missense_variant 0.38 rifampicin
rpoA 3877905 c.603A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoA 3877908 c.600T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038551 c.2154C>G synonymous_variant 0.47 pyrazinamide
clpC1 4039454 c.1251A>T synonymous_variant 0.27 pyrazinamide
clpC1 4040693 c.12A>T synonymous_variant 0.3 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R