TB-Profiler result

Run: SRR6785527
Summary

Run ID: SRR6785527

Sample name:

Date: 2024-04-15T01:04:35.115104

Number of reads: 2855538

Percentage reads mapped: 83.2

Median coverage: 71.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.97
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.98
lineage2.2 East-Asian (Beijing) RD105;RD207 0.98
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
gyrA 6670 c.-632G>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6673 c.-629A>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6676 c.-626T>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6700 c.-602T>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6703 c.-599G>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6709 c.-593A>G upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 6712 c.-590G>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrB 6728 c.1489_1491delCTAinsTG frameshift_variant&stop_gained 0.15 levofloxacin Uncertain significance
moxifloxacin
gyrA 6742 c.-560A>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrB 6745 c.1506T>G synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6751 c.-551G>C upstream_gene_variant 0.13 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7451 c.150C>G synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7457 c.156T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7475 c.174A>G synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7480 p.Phe60Tyr missense_variant 0.13 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8372 c.1071G>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 8375 c.1074G>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 8382 p.Leu361Met missense_variant 0.14 levofloxacin
moxifloxacin
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 0.95 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575770 c.423G>A synonymous_variant 0.14 ethionamide
isoniazid
mshA 575771 p.Val142Ser missense_variant 0.14 ethionamide
isoniazid
mshA 575779 c.432A>G synonymous_variant 0.16 ethionamide
isoniazid
mshA 575782 c.435G>C synonymous_variant 0.16 ethionamide
isoniazid
mshA 575821 c.474G>C synonymous_variant 0.16 ethionamide
isoniazid
mshA 575824 c.477T>G synonymous_variant 0.19 ethionamide
isoniazid
mshA 575830 c.483C>G synonymous_variant 0.17 ethionamide
isoniazid
mshA 575833 c.486C>G synonymous_variant 0.18 ethionamide
isoniazid
mshA 575845 c.498C>T synonymous_variant 0.18 ethionamide
isoniazid Not assoc w R - Interim
mshA 575884 c.537G>C synonymous_variant 0.14 ethionamide
isoniazid
mshA 575887 c.540G>C synonymous_variant 0.14 ethionamide
isoniazid
mshA 575907 p.Ala187Val missense_variant 0.89 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.99 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.91 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.95 ethionamide Uncertain significance
hadA 732305 p.Ile126Val missense_variant 0.14 isoniazid
hadA 732308 p.Val127Ile missense_variant 0.15 isoniazid
hadA 732321 p.Glu131Ala missense_variant 0.13 isoniazid
hadA 732329 p.Leu134Val missense_variant 0.17 isoniazid Uncertain significance
hadA 732337 c.408G>A synonymous_variant 0.18 isoniazid
hadA 732378 c.450_452dupAGA disruptive_inframe_insertion 0.19 isoniazid
hadA 732396 p.Gly156Ala missense_variant 0.23 isoniazid
hadA 732398 p.Ala157Thr missense_variant 0.23 isoniazid
nusG 734424 c.171G>A synonymous_variant 0.13 rifampicin
nusG 734442 c.189G>A synonymous_variant 0.14 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760361 c.555T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760370 c.564C>G synonymous_variant 0.14 rifampicin
rpoB 760381 p.Thr192Met missense_variant 0.14 rifampicin
rpoB 760406 c.600G>C synonymous_variant 0.14 rifampicin
rpoB 760412 c.606C>G synonymous_variant 0.14 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760591 p.Val262Ala missense_variant 0.13 rifampicin
rpoB 760982 c.1176G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760991 c.1185G>C synonymous_variant 0.16 rifampicin
rpoB 761006 c.1200C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.15 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761306 c.1500C>G synonymous_variant 0.17 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.95 rifampicin Not assoc w R
rpoC 763456 c.87A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.19 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.15 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.24 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.25 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.25 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.26 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.23 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.24 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763816 c.447C>G synonymous_variant 0.2 rifampicin
rpoC 763835 p.Ala156Met missense_variant 0.17 rifampicin
rpoC 763853 p.Val162Ile missense_variant 0.16 rifampicin
rpoC 763858 c.489A>G synonymous_variant 0.16 rifampicin
rpoC 764112 p.Tyr248Phe missense_variant 0.14 rifampicin
rpoC 764116 c.747C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764338 c.969G>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764353 c.984G>C synonymous_variant 0.16 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764381 p.Ser338Thr missense_variant 0.12 rifampicin
rpoC 764827 c.1458G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.19 rifampicin
rpoC 764932 c.1563C>A synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764935 c.1566T>C synonymous_variant 0.19 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 765319 c.1950A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765529 c.2160C>T synonymous_variant 0.13 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.16 rifampicin
rpoC 765751 c.2382C>G synonymous_variant 0.15 rifampicin
rpoC 765753 p.Asp795Ala missense_variant 0.14 rifampicin Uncertain significance
rpoC 765772 c.2403C>G synonymous_variant 0.15 rifampicin
rpoC 765784 c.2415C>G synonymous_variant 0.16 rifampicin
rpoC 765811 c.2442T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765814 c.2445A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765826 c.2457T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765835 c.2466C>T synonymous_variant 0.15 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 0.17 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.17 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765937 c.2568T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>G synonymous_variant 0.15 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766010 p.Ser881Thr missense_variant 0.13 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.15 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.19 rifampicin
rpoC 766801 c.3432C>G synonymous_variant 0.19 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.15 rifampicin
rpoC 766972 c.3603G>C synonymous_variant 0.14 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.23 rifampicin
rpoC 767014 c.3645G>C synonymous_variant 0.23 rifampicin
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.24 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.22 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.16 rifampicin
rpoC 767158 c.3789T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767180 p.Ala1271Gln missense_variant 0.15 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767206 c.3837C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767209 c.3840T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 767212 c.3843G>C synonymous_variant 0.14 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.96 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.95 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.98 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781832 c.273T>C synonymous_variant 0.15 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.16 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.15 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.15 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.15 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.15 streptomycin
rpsL 781877 c.318T>C synonymous_variant 0.16 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.15 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.15 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.15 streptomycin
rplC 801402 c.594T>C synonymous_variant 0.17 linezolid
rplC 801405 c.597T>C synonymous_variant 0.17 linezolid
rplC 801423 c.615G>C synonymous_variant 0.15 linezolid
rplC 801426 c.618C>G synonymous_variant 0.15 linezolid
rplC 801427 p.Met207Val missense_variant 0.15 linezolid
rplC 801438 c.630T>C synonymous_variant 0.15 linezolid
rplC 801442 p.Ile212Val missense_variant 0.17 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.98 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254623 c.-89C>A upstream_gene_variant 0.15 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1303860 c.930A>C synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fbiC 1303884 c.954T>G synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1303905 c.975G>C synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1303914 c.984C>G synonymous_variant 0.19 clofazimine
pretomanid
delamanid
fbiC 1303920 c.990C>T synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1303971 c.1041T>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303980 c.1050G>A synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1303998 c.1068T>G synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1304174 p.Val415Ala missense_variant 0.13 clofazimine
pretomanid
delamanid
fbiC 1304184 c.1254G>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1304187 c.1257T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1304208 c.1278C>T synonymous_variant 0.14 clofazimine
pretomanid
delamanid
sigE 1364706 c.294G>A synonymous_variant 0.98 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 1475061 n.1404C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rpsA 1833838 c.297G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.19 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.2 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.24 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.31 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.28 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.26 pyrazinamide
rpsA 1833971 c.430C>T synonymous_variant 0.18 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.19 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.16 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
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 0.97 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.17 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.18 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2782948 c.1095A>G synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782957 c.1086A>G synonymous_variant 0.17 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2782966 c.1077C>A synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782969 c.1074A>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782972 c.1071G>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782981 c.1062G>C synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782984 c.1059T>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782990 c.1053C>G synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783002 c.1041T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783008 c.1035C>G synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783015 p.Ser343Thr missense_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783665 c.378A>G synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783674 c.369T>C synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783700 p.Thr115Ser missense_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783718 c.325T>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783719 c.324A>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783751 p.Ile98Val missense_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783758 p.Asp95Glu missense_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783761 c.282G>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783766 p.Met93Leu missense_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784518 c.-476C>T upstream_gene_variant 0.96 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2752c 3065109 c.1081_1083delAGAinsCC frameshift_variant&missense_variant 0.14 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv2752c 3065115 c.1077C>A synonymous_variant 0.14 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065142 c.1050A>C synonymous_variant 0.14 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3065146 p.Phe349Tyr missense_variant 0.13 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065151 c.1041G>C synonymous_variant 0.15 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyX 3067457 c.489C>G synonymous_variant 0.18 para-aminosalicylic_acid
thyX 3067465 p.Ile161Val missense_variant 0.2 para-aminosalicylic_acid
thyX 3067475 c.471A>G synonymous_variant 0.19 para-aminosalicylic_acid
thyX 3067490 c.456C>G synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067493 c.453A>G synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067530 p.Ala139Ser missense_variant 0.17 para-aminosalicylic_acid
thyX 3067545 p.Glu134Ala missense_variant 0.17 para-aminosalicylic_acid
thyX 3067549 p.Thr133Ala missense_variant 0.16 para-aminosalicylic_acid
thyX 3067559 c.387C>G synonymous_variant 0.13 para-aminosalicylic_acid
thyX 3067781 c.165C>A synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067793 c.153T>C synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067799 c.147G>A synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067802 c.144C>G synonymous_variant 0.19 para-aminosalicylic_acid
thyX 3067814 c.132T>C synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067850 c.96A>C synonymous_variant 0.17 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625572 p.Thr348Ser missense_variant 0.14 bedaquiline
rifampicin
lpqB 3625579 c.-669A>G upstream_gene_variant 0.14 bedaquiline
rifampicin
lpqB 3625594 c.-684T>C upstream_gene_variant 0.15 bedaquiline
rifampicin
lpqB 3625602 c.-692T>C upstream_gene_variant 0.17 bedaquiline
rifampicin
lpqB 3625612 c.-702G>C upstream_gene_variant 0.19 bedaquiline
rifampicin
mtrB 3625616 p.Arg333Ala missense_variant 0.19 bedaquiline
rifampicin
lpqB 3625624 c.-714C>G upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrB 3625636 c.978C>G synonymous_variant 0.15 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625797 p.Val273Met missense_variant 0.13 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626840 c.-227C>G upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrA 3626846 c.504G>A synonymous_variant 0.15 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626858 c.-245A>G upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626861 c.-248C>G upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626866 c.-253T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626876 c.-263A>G upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626885 c.-272A>C upstream_gene_variant 0.14 bedaquiline
rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
clpC1 4040291 c.414G>C synonymous_variant 0.19 pyrazinamide
clpC1 4040318 c.387C>G synonymous_variant 0.18 pyrazinamide
clpC1 4040330 c.375C>G synonymous_variant 0.15 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.99 ethambutol Not assoc w R
embB 4247491 c.978G>C synonymous_variant 0.14 ethambutol
embB 4247497 c.984T>C synonymous_variant 0.15 ethambutol
embB 4247512 c.999T>C synonymous_variant 0.16 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.96 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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R
gid 4408107 p.Glu32Asp missense_variant 0.95 streptomycin Uncertain significance