TB-Profiler result

Run: ERR3275215
Summary

Run ID: ERR3275215

Sample name:

Date: 2024-04-16T07:05:20.942043

Number of reads: 4830751

Percentage reads mapped: 99.45

Median coverage: 68.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.98
lineage4.1.2 Euro-American None 0.99
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.99
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB c.1327_1329delTTGinsCC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid
ethambutol
pyrazinamide
streptomycin rrs n.462C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fbiC c.859_861delATCinsGG 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
rpoB 761133 c.1327_1329delTTGinsCC frameshift_variant&missense_variant 0.13 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
fbiC 1303789 c.859_861delATCinsGG frameshift_variant&missense_variant 0.15 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance 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
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 8375 c.1074G>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 8391 c.1090_1092delTATinsCC frameshift_variant&missense_variant 0.16 levofloxacin
moxifloxacin
gyrA 8399 c.1098T>C synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8420 c.1119T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8423 c.1122G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8442 c.1141C>T synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8453 c.1152A>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8462 c.1161A>G synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491542 c.760T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491547 c.765A>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491550 c.768T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491591 p.Lys270Met missense_variant 0.94 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.94 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.94 ethionamide Uncertain significance
hadA 732396 p.Gly156Ala missense_variant 0.14 isoniazid
hadA 732398 p.Ala157Thr missense_variant 0.14 isoniazid
nusG 734481 c.228C>G synonymous_variant 0.15 rifampicin
nusG 734499 c.246G>C synonymous_variant 0.14 rifampicin
nusG 734532 c.279A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
nusG 734541 c.288A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
nusG 734559 c.306T>C synonymous_variant 0.13 rifampicin
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 760328 c.522G>C synonymous_variant 0.15 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.13 rifampicin
rpoB 760337 c.531C>G synonymous_variant 0.14 rifampicin
rpoB 760361 c.555T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760376 p.Asp190Glu missense_variant 0.16 rifampicin Uncertain significance
rpoB 760406 c.600G>C synonymous_variant 0.15 rifampicin
rpoB 760418 c.612G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760424 c.618C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760475 c.669A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760522 p.Ser239Asn missense_variant 0.21 rifampicin Uncertain significance
rpoB 760532 c.726T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760533 p.Val243Thr missense_variant 0.2 rifampicin
rpoB 760547 c.741G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 760563 p.Arg253Met missense_variant 0.19 rifampicin Uncertain significance
rpoB 760591 p.Val262Ala missense_variant 0.23 rifampicin
rpoB 760611 c.805T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 760634 c.828T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 760655 c.849A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.19 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760817 c.1011A>G synonymous_variant 0.13 rifampicin
rpoB 760820 c.1014T>C synonymous_variant 0.13 rifampicin
rpoB 760845 p.Thr347Pro missense_variant 0.13 rifampicin
rpoB 760869 p.Val355Ile missense_variant 0.15 rifampicin Uncertain significance
rpoB 760886 c.1080A>G synonymous_variant 0.16 rifampicin
rpoB 760919 c.1113C>G synonymous_variant 0.13 rifampicin
rpoB 760970 c.1164G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760982 c.1176G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760991 c.1185G>C synonymous_variant 0.14 rifampicin
rpoB 761015 c.1209G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.16 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761051 c.1245G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>A synonymous_variant 0.17 rifampicin
rpoB 761057 c.1251G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761063 c.1257C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761222 c.1416G>C synonymous_variant 0.16 rifampicin
rpoB 761249 c.1443A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763076 c.-294C>G upstream_gene_variant 0.17 rifampicin
rpoB 763085 c.3279C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763148 c.-222G>C upstream_gene_variant 0.15 rifampicin
rpoC 763158 c.-212C>T upstream_gene_variant 0.17 rifampicin
rpoB 763166 c.3360A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763169 c.-201A>G upstream_gene_variant 0.15 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764083 c.714A>G synonymous_variant 0.14 rifampicin
rpoC 764101 c.732C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764530 c.1161C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.14 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.16 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.16 rifampicin
rpoC 764923 c.1554A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764932 c.1563C>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.14 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.99 rifampicin Not assoc w R
rpoC 765541 c.2172C>G synonymous_variant 0.13 rifampicin
rpoC 765556 c.2187G>C synonymous_variant 0.14 rifampicin
rpoC 765559 c.2190G>C synonymous_variant 0.14 rifampicin
rpoC 765577 c.2208G>C synonymous_variant 0.13 rifampicin
rpoC 765578 c.2209C>T synonymous_variant 0.13 rifampicin
rpoC 765583 c.2214G>T synonymous_variant 0.13 rifampicin
rpoC 766607 c.3238_3240delATCinsCG frameshift_variant&missense_variant 0.16 rifampicin
rpoC 766630 c.3261G>C synonymous_variant 0.21 rifampicin
rpoC 766645 c.3276A>G synonymous_variant 0.2 rifampicin
rpoC 766651 c.3282T>C synonymous_variant 0.18 rifampicin
rpoC 766657 c.3288A>G synonymous_variant 0.17 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.17 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.16 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.16 rifampicin
rpoC 766894 c.3525T>C synonymous_variant 0.14 rifampicin
rpoC 766895 c.3526T>C synonymous_variant 0.14 rifampicin
rpoC 766978 c.3609C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 766996 c.3627C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAGC synonymous_variant 0.17 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 767074 c.3705T>C synonymous_variant 0.2 rifampicin
rpoC 767119 c.3750A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>G synonymous_variant 0.16 rifampicin
rpoC 767167 c.3798C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781715 c.156T>C synonymous_variant 0.14 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.13 streptomycin
fbiC 1303746 c.816T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303749 c.819G>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303752 c.822A>G synonymous_variant 0.16 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1303755 c.825T>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303785 c.855G>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303818 c.888C>G synonymous_variant 0.12 clofazimine
pretomanid
delamanid
fbiC 1303846 p.Phe306Val missense_variant 0.13 clofazimine
pretomanid
delamanid
fbiC 1303854 c.924T>C synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fbiC 1303860 c.930A>C synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fbiC 1303881 c.951G>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303884 c.954T>G synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303911 c.981G>C synonymous_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1303914 c.984C>G synonymous_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1303920 c.990C>G synonymous_variant 0.21 clofazimine
pretomanid
delamanid
fbiC 1303923 c.993C>T synonymous_variant 0.22 clofazimine
pretomanid
delamanid
fbiC 1303929 c.999G>C synonymous_variant 0.21 clofazimine
pretomanid
delamanid
fbiC 1303947 c.1017T>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303948 p.Gly340Arg missense_variant 0.16 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1473944 n.287G>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1473945 n.288T>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.15 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 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474962 n.1306delG non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475271 n.1614A>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475273 n.1616T>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
inhA 1674624 c.423A>C synonymous_variant 0.16 ethionamide
isoniazid
inhA 1674627 c.426T>G synonymous_variant 0.15 ethionamide
isoniazid
inhA 1674630 c.429C>G synonymous_variant 0.15 ethionamide
isoniazid
inhA 1674636 c.435C>G synonymous_variant 0.16 ethionamide
isoniazid
inhA 1674654 c.453G>C synonymous_variant 0.15 ethionamide
isoniazid
rpsA 1833787 c.246C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833790 c.249T>A synonymous_variant 0.14 pyrazinamide
rpsA 1833799 c.258C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.15 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.16 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.15 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.17 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834225 c.684C>G synonymous_variant 0.13 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834261 c.720A>C synonymous_variant 0.15 pyrazinamide
rpsA 1834264 c.723G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834297 c.756C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.15 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
rpsA 1834528 c.987T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834555 c.1014T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834558 c.1017C>G synonymous_variant 0.15 pyrazinamide
tsnR 1853370 c.-236_-234delGCAinsTG upstream_gene_variant 0.13 linezolid
tsnR 1853384 c.-222G>C upstream_gene_variant 0.13 linezolid
tsnR 1853387 c.-219T>G upstream_gene_variant 0.13 linezolid
tsnR 1853394 c.-212_-211delCTinsGC upstream_gene_variant 0.13 linezolid
tsnR 1853420 c.-186T>G upstream_gene_variant 0.15 linezolid
tsnR 1853429 c.-177G>C upstream_gene_variant 0.14 linezolid
tsnR 1853432 c.-174G>C upstream_gene_variant 0.14 linezolid
tsnR 1853447 c.-159C>G upstream_gene_variant 0.14 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
katG 2154907 p.Glu402Ala missense_variant 1.0 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2517947 c.-168C>T upstream_gene_variant 0.16 isoniazid
kasA 2517974 c.-141T>C upstream_gene_variant 0.15 isoniazid
kasA 2517989 c.-126T>C upstream_gene_variant 0.14 isoniazid
kasA 2517992 c.-123C>G upstream_gene_variant 0.13 isoniazid
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
kasA 2518561 c.447T>C synonymous_variant 0.15 isoniazid
kasA 2518567 c.453G>C synonymous_variant 0.15 isoniazid
kasA 2518570 c.456G>C synonymous_variant 0.15 isoniazid
kasA 2518574 c.460_462delATCinsGG frameshift_variant&missense_variant 0.15 isoniazid
kasA 2518588 c.474T>C synonymous_variant 0.14 isoniazid
kasA 2518591 c.477G>C synonymous_variant 0.14 isoniazid
kasA 2518816 c.702C>A synonymous_variant 0.13 isoniazid
Rv2477c 2783002 c.1041T>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783008 c.1035C>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783013 c.1030T>C synonymous_variant 0.13 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 2783015 p.Ser343Thr missense_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783020 c.1023G>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783040 p.Ala335Thr missense_variant 0.17 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2477c 2783059 c.984T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783062 c.981C>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783068 p.Asp325Glu missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783077 c.966T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.22 capreomycin Uncertain significance
thyA 3073977 c.495A>G synonymous_variant 0.13 para-aminosalicylic_acid
thyA 3074001 c.471C>G synonymous_variant 0.15 para-aminosalicylic_acid
thyA 3074004 c.468T>C synonymous_variant 0.15 para-aminosalicylic_acid
ald 3086767 c.-53A>T upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625750 c.864G>A synonymous_variant 0.13 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625755 p.Ala287Thr missense_variant 0.15 bedaquiline
rifampicin Uncertain significance
mtrB 3625762 c.852A>G synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625765 c.849C>G synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625797 p.Val273Met missense_variant 0.17 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625806 c.808A>C synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625837 c.777C>G synonymous_variant 0.15 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625840 c.-930A>G upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3625852 c.762A>G synonymous_variant 0.12 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626912 c.438T>C synonymous_variant 0.12 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627756 c.-407A>T upstream_gene_variant 1.0 bedaquiline
rifampicin
rpoA 3878346 c.162T>C synonymous_variant 0.12 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.14 rifampicin
rpoA 3878391 c.117T>C synonymous_variant 0.16 rifampicin
rpoA 3878396 c.112C>T synonymous_variant 0.17 rifampicin
rpoA 3878436 c.72A>G synonymous_variant 0.21 rifampicin
rpoA 3878442 c.66G>C synonymous_variant 0.2 rifampicin
rpoA 3878454 c.54A>C synonymous_variant 0.2 rifampicin
rpoA 3878472 p.Asp12Glu missense_variant 0.17 rifampicin
rpoA 3878478 c.30C>G synonymous_variant 0.15 rifampicin
rpoA 3878490 c.18C>A synonymous_variant 0.15 rifampicin
rpoA 3878496 c.12A>T synonymous_variant 0.16 rifampicin
rpoA 3879151 c.-644C>T upstream_gene_variant 0.99 rifampicin
clpC1 4038740 c.1965G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038755 c.1950G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.13 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.14 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.15 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.12 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.15 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038989 c.1716T>C synonymous_variant 0.12 pyrazinamide
clpC1 4039682 c.1023C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039685 c.1020C>T synonymous_variant 0.14 pyrazinamide
clpC1 4039748 c.957G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.13 pyrazinamide
embC 4239298 c.-565C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embA 4245137 c.1905T>C synonymous_variant 0.13 ethambutol
embA 4245149 c.1917C>G synonymous_variant 0.17 ethambutol
embB 4248277 c.1764G>C synonymous_variant 0.13 ethambutol
ubiA 4269919 c.-86T>G upstream_gene_variant 1.0 ethambutol
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