TB-Profiler result

Run: SRR1181328
Summary

Run ID: SRR1181328

Sample name:

Date: 2024-10-04T13:21:42.481804

Number of reads: 3363989

Percentage reads mapped: 79.09

Median coverage: 77.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.99
lineage2.2 East-Asian (Beijing) RD105;RD207 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 embB p.His312Arg Mutation from literature
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
embB 4247448 p.His312Arg missense_variant 0.17 ethambutol Mutation from literature
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
dnaA 1245 c.1245G>C synonymous_variant 0.18 isoniazid Not assoc w R - Interim
dnaA 1254 c.1254T>C synonymous_variant 0.18 isoniazid
dnaA 1278 c.1278T>C synonymous_variant 0.17 isoniazid
gyrB 6250 c.1011A>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6307 c.1068T>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6700 c.-602T>C upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrA 6703 c.-599G>C upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrA 6706 c.-596G>A upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6709 c.-593A>G upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrB 6721 c.1482C>T synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
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 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7784 c.483A>G synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7799 c.498A>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8121 c.820T>C synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 8156 c.855T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8168 c.867A>G synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8177 c.876A>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8324 c.1023T>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8339 c.1038A>G synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8340 p.Ala347Ser missense_variant 0.15 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8375 c.1074G>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 8603 c.1302A>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8609 c.1308G>C synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8619 c.1318T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8645 c.1344C>T synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8655 p.Ile452Val missense_variant 0.19 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 490863 c.81C>A synonymous_variant 0.13 pretomanid
delamanid
clofazimine
fgd1 491542 c.760T>C synonymous_variant 0.14 pretomanid
delamanid
clofazimine
fgd1 491547 c.765A>C synonymous_variant 0.16 pretomanid
delamanid
clofazimine
fgd1 491742 c.960T>C synonymous_variant 0.99 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.88 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 575916 p.Asp190Ala missense_variant 0.13 isoniazid
ethionamide
ccsA 620625 p.Ile245Met missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.99 ethionamide Uncertain significance
hadA 731774 c.-156T>C upstream_gene_variant 0.22 isoniazid
nusG 734409 c.156T>C synonymous_variant 0.14 rifampicin
nusG 734589 c.336G>C synonymous_variant 0.14 rifampicin
nusG 734781 c.528A>G synonymous_variant 0.22 rifampicin
nusG 734784 c.531G>A synonymous_variant 0.22 rifampicin
nusG 734790 c.537G>C synonymous_variant 0.13 rifampicin
rpoB 760184 c.378A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760235 c.429T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760591 p.Val262Ala missense_variant 0.13 rifampicin
rpoB 761015 c.1209G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761027 c.1221A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761097 c.1291_1292delAGinsTC synonymous_variant 0.18 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.18 rifampicin
rpoB 761249 c.1443A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761492 c.1686G>C synonymous_variant 0.17 rifampicin
rpoB 761537 c.1731C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761561 c.1755C>G synonymous_variant 0.17 rifampicin
rpoB 761564 c.1758G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.14 rifampicin Uncertain significance
rpoB 762185 c.2379G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762254 c.2448T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 762410 c.-960T>C upstream_gene_variant 0.15 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762470 c.2664G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 762983 c.-387C>A upstream_gene_variant 0.14 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.23 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 0.26 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 763076 c.-294C>T upstream_gene_variant 0.14 rifampicin
rpoB 763085 c.3279C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>G synonymous_variant 0.19 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763765 c.396T>C synonymous_variant 0.16 rifampicin
rpoC 763781 p.Ser138Ala missense_variant 0.18 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763836 p.Ala156Val missense_variant 0.15 rifampicin
rpoC 763855 c.486C>T synonymous_variant 0.16 rifampicin
rpoC 763858 c.489A>G synonymous_variant 0.14 rifampicin
rpoC 763888 c.519G>T synonymous_variant 0.14 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.19 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.19 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764500 c.1131C>G synonymous_variant 0.18 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764578 c.1209C>G synonymous_variant 0.16 rifampicin
rpoC 764668 c.1299C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764815 c.1446A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764833 c.1464A>G synonymous_variant 0.14 rifampicin
rpoC 765547 c.2178C>A synonymous_variant 0.19 rifampicin
rpoC 765556 c.2187G>C synonymous_variant 0.18 rifampicin
rpoC 765562 c.2193G>C synonymous_variant 0.17 rifampicin
rpoC 765685 c.2316G>A synonymous_variant 0.14 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765883 c.2514C>G synonymous_variant 0.18 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.19 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765952 c.2583G>C synonymous_variant 0.14 rifampicin
rpoC 766381 c.3012C>T synonymous_variant 0.16 rifampicin
rpoC 766384 c.3015A>G synonymous_variant 0.15 rifampicin
rpoC 766408 c.3039C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 766426 c.3057C>T synonymous_variant 0.19 rifampicin
rpoC 766543 c.3174C>T synonymous_variant 0.2 rifampicin
rpoC 766573 c.3204T>C synonymous_variant 0.18 rifampicin
rpoC 766579 c.3210C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766585 c.3216T>C synonymous_variant 0.21 rifampicin
rpoC 766594 c.3225G>C synonymous_variant 0.21 rifampicin
rpoC 766607 p.Ile1080Leu missense_variant 0.18 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.13 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.19 rifampicin
rpoC 766792 c.3423C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766795 c.3426C>T synonymous_variant 0.15 rifampicin
rpoC 766801 c.3432C>T synonymous_variant 0.16 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766843 c.3474T>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.17 rifampicin
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.19 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.2 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767200 c.3831G>A synonymous_variant 0.17 rifampicin
rpoC 767209 c.3840T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 767221 c.3852C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 767230 c.3861G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767233 c.3864T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 767264 p.Ala1299Gln missense_variant 0.16 rifampicin
rpoC 767275 c.3906T>A synonymous_variant 0.15 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 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.98 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781728 c.169T>C synonymous_variant 0.14 streptomycin
rplC 800567 c.-242A>G upstream_gene_variant 0.14 linezolid
rplC 800579 c.-230C>T upstream_gene_variant 0.14 linezolid
rplC 800582 c.-227C>G upstream_gene_variant 0.15 linezolid
rplC 800648 c.-161A>C upstream_gene_variant 0.15 linezolid
rplC 800693 c.-116A>C upstream_gene_variant 0.18 linezolid
rplC 800714 c.-95C>T upstream_gene_variant 0.18 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.18 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.19 linezolid
rplC 800877 c.69A>C synonymous_variant 0.14 linezolid
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 1303545 c.615A>G synonymous_variant 0.15 pretomanid
delamanid
clofazimine
fbiC 1304832 c.1902C>T synonymous_variant 0.14 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
sigE 1364889 c.477A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471935 n.90T>C non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471970 n.125G>A non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472040 n.195T>C non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.16 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473731 n.74T>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1473887 n.230T>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474061 n.404T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.16 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 1474249 n.592G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475487 n.1830C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674015 c.-187C>A upstream_gene_variant 0.17 isoniazid
ethionamide
inhA 1674018 c.-184G>C upstream_gene_variant 0.17 isoniazid
ethionamide
inhA 1674024 c.-178T>C upstream_gene_variant 0.16 isoniazid
ethionamide
rpsA 1833589 c.48A>T synonymous_variant 0.18 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.15 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.18 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834249 c.708T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834348 c.807T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834396 c.855G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.18 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.19 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.22 pyrazinamide
rpsA 1834495 c.954G>A synonymous_variant 0.19 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834615 c.1074C>T synonymous_variant 0.19 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.17 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.17 pyrazinamide
tsnR 1853574 c.-32T>C upstream_gene_variant 1.0 linezolid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2064269 c.460A>C synonymous_variant 0.14 kanamycin
capreomycin
streptomycin
amikacin
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
Rv2477c 2783860 c.183T>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783883 c.160T>C synonymous_variant 0.22 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.97 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3626846 c.504G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626852 c.-239G>A upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3626866 c.-253T>C upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3626885 c.-272A>G upstream_gene_variant 0.13 rifampicin
bedaquiline
mtrB 3626890 c.-277T>C upstream_gene_variant 0.16 rifampicin
bedaquiline
mtrA 3626912 c.438T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3877587 c.921A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3878157 c.351C>G synonymous_variant 0.14 rifampicin
rpoA 3878283 p.Glu75Asp missense_variant 0.21 rifampicin Uncertain significance
rpoA 3878295 c.213A>G synonymous_variant 0.17 rifampicin
rpoA 3878298 c.210A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878853 c.-346G>A upstream_gene_variant 0.2 rifampicin
rpoA 3878878 c.-371T>C upstream_gene_variant 0.2 rifampicin Uncertain significance
rpoA 3878909 c.-402A>G upstream_gene_variant 0.29 rifampicin
rpoA 3878914 c.-407T>C upstream_gene_variant 0.27 rifampicin Uncertain significance
rpoA 3878938 c.-431T>C upstream_gene_variant 0.22 rifampicin
rpoA 3878947 c.-440G>C upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoA 3879088 c.-581A>C upstream_gene_variant 0.16 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.17 rifampicin
rpoA 3879121 c.-614T>G upstream_gene_variant 0.16 rifampicin
rpoA 3879154 c.-647T>C upstream_gene_variant 0.2 rifampicin
rpoA 3879160 c.-653A>G upstream_gene_variant 0.18 rifampicin
clpC1 4038350 c.2355C>G synonymous_variant 0.17 pyrazinamide
clpC1 4038356 c.2349T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038359 c.2346A>G synonymous_variant 0.16 pyrazinamide
clpC1 4038368 c.2337T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038596 c.2109A>G synonymous_variant 0.16 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038980 c.1725C>T synonymous_variant 0.15 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.14 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.16 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.15 pyrazinamide
clpC1 4039442 c.1263A>G synonymous_variant 0.14 pyrazinamide
clpC1 4040551 c.154T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
embC 4240783 c.921G>C synonymous_variant 0.13 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4245683 c.-831C>T upstream_gene_variant 0.13 ethambutol
embB 4246567 c.54G>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247470 c.957T>C synonymous_variant 0.14 ethambutol
embB 4247497 c.984T>C synonymous_variant 0.16 ethambutol
embB 4247500 c.987C>G synonymous_variant 0.15 ethambutol
embB 4247512 c.999T>C synonymous_variant 0.15 ethambutol
aftB 4267580 c.1257G>A synonymous_variant 0.14 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.9 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 4407588 c.615A>G synonymous_variant 0.99 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R