TB-Profiler result

Run: ERR4796472
Summary

Run ID: ERR4796472

Sample name:

Date: 2025-02-11T12:42:39.453702

Number of reads: 855762

Percentage reads mapped: 62.56

Median coverage: 25.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
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 rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol embA c.-11C>A Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Ala504Val Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Ala504Val Assoc w R - Interim
gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
gyrB 6750 p.Ala504Val missense_variant 1.0 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7570 p.Ala90Val missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
pncA 2289162 p.Leu27Pro missense_variant 1.0 pyrazinamide Assoc w R
embA 4243222 c.-11C>A upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol Assoc w R
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
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 1.0 ethionamide Uncertain significance
rpoB 762002 c.2196C>G synonymous_variant 0.23 rifampicin
rpoB 762003 p.Asn733Gln missense_variant 0.24 rifampicin
rpoB 762011 c.2205G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762017 c.2211A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762020 p.Glu738Asp missense_variant 0.25 rifampicin
rpoB 762023 c.2217C>T synonymous_variant 0.26 rifampicin
rpoB 762026 c.2220G>C synonymous_variant 0.26 rifampicin
rpoB 762041 c.2235C>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 762047 c.2241G>A synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 762062 c.2256T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 762071 c.2265C>T synonymous_variant 0.34 rifampicin
rpoB 762083 c.2277T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.33 rifampicin Uncertain significance
rpoB 762143 c.2337T>C synonymous_variant 0.24 rifampicin
rpoB 762158 c.2352G>A synonymous_variant 0.29 rifampicin
rpoB 762161 c.2355C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762170 c.2364C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762221 c.2415G>A synonymous_variant 0.21 rifampicin
rpoB 762233 c.2427G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762236 c.2430G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763049 c.-321G>A upstream_gene_variant 0.21 rifampicin
rpoB 763053 c.3247T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763444 c.75T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763453 c.84C>G synonymous_variant 0.32 rifampicin
rpoC 763456 c.87A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 763459 c.90G>A synonymous_variant 0.32 rifampicin
rpoC 763468 c.99G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763505 c.136C>T synonymous_variant 0.22 rifampicin
rpoC 763528 c.159G>T synonymous_variant 0.24 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.24 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.22 rifampicin
rpoC 763537 c.168C>G synonymous_variant 0.22 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763558 c.189C>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763597 c.228G>A synonymous_variant 0.17 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764593 c.1224C>T synonymous_variant 0.28 rifampicin
rpoC 764626 c.1257C>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764677 c.1308C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764680 c.1311G>A synonymous_variant 0.2 rifampicin
rpoC 764701 c.1332C>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764722 c.1353G>C synonymous_variant 0.34 rifampicin
rpoC 764728 c.1359G>A synonymous_variant 0.34 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764779 c.1410G>A synonymous_variant 0.36 rifampicin
rpoC 764780 c.1411_1412delAGinsTC synonymous_variant 0.36 rifampicin
rpoC 764785 c.1416C>G synonymous_variant 0.34 rifampicin
rpoC 764791 c.1422C>G synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>G synonymous_variant 0.39 rifampicin
rpoC 764809 c.1440C>G synonymous_variant 0.41 rifampicin
rpoC 764812 c.1443C>G synonymous_variant 0.4 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 765772 c.2403C>G synonymous_variant 0.21 rifampicin
rpoC 765781 c.2412C>T synonymous_variant 0.24 rifampicin
rpoC 765784 c.2415C>G synonymous_variant 0.24 rifampicin
rpoC 765793 c.2424C>G synonymous_variant 0.26 rifampicin
rpoC 765796 c.2427C>T synonymous_variant 0.26 rifampicin
rpoC 765811 c.2442T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 765814 c.2445A>T synonymous_variant 0.3 rifampicin
rpoC 765817 c.2448G>C synonymous_variant 0.3 rifampicin
rpoC 765820 c.2451G>C synonymous_variant 0.3 rifampicin
rpoC 765823 c.2454C>G synonymous_variant 0.32 rifampicin
rpoC 765844 c.2475C>G synonymous_variant 0.33 rifampicin
rpoC 765875 p.Val836Ile missense_variant 0.32 rifampicin Uncertain significance
rpoC 765880 c.2511G>A synonymous_variant 0.32 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.29 rifampicin
rpoC 766488 p.Pro1040Arg missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781817 c.258G>T synonymous_variant 0.22 streptomycin
rpsL 781829 c.270G>T synonymous_variant 0.22 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.22 streptomycin
rpsL 781853 c.294C>T synonymous_variant 0.23 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.21 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.21 streptomycin
rpsL 781880 c.321C>G synonymous_variant 0.24 streptomycin
rpsL 781889 c.330C>T synonymous_variant 0.22 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.22 streptomycin
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471978 n.133C>T non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1471985 n.140T>C non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472486 n.641A>G non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472497 n.652G>T non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472580 n.735C>A non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472873 n.1028C>T non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472875 n.1030T>G non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.49 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.62 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.58 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.58 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.46 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.35 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474135 n.478G>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474359 n.702C>G non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474402 n.745T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474412 n.756_768delACCCACACGCGCA non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1474427 n.770A>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1474429 n.773_783delCGCGTGTGAAT non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1474444 n.787G>C non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475735 n.2078T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475760 n.2103_2110delCCGCAAGGinsGCTTCGGC non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.61 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.75 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476058 n.2401T>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476103 n.2446C>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid
rrl 1476105 n.2450delA non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476110 n.2453G>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.56 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.52 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833646 c.105T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
rpsA 1833652 c.111C>T synonymous_variant 0.17 pyrazinamide
rpsA 1833664 c.123C>A synonymous_variant 0.17 pyrazinamide
rpsA 1833679 c.138G>C synonymous_variant 0.21 pyrazinamide
rpsA 1833685 c.144G>C synonymous_variant 0.25 pyrazinamide
rpsA 1833694 c.153G>C synonymous_variant 0.27 pyrazinamide
rpsA 1833697 c.156C>G synonymous_variant 0.27 pyrazinamide
rpsA 1833769 c.228C>G synonymous_variant 0.27 pyrazinamide
rpsA 1833991 c.450C>A synonymous_variant 0.3 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.29 pyrazinamide
rpsA 1834012 c.471G>C synonymous_variant 0.29 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.29 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.29 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.25 pyrazinamide
rpsA 1834034 p.Ile165Val missense_variant 0.23 pyrazinamide
rpsA 1834093 c.552G>T synonymous_variant 0.25 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.29 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834327 c.786G>T synonymous_variant 0.34 pyrazinamide
rpsA 1834340 p.Met267Leu missense_variant 0.37 pyrazinamide Uncertain significance
rpsA 1834348 c.807T>C synonymous_variant 0.33 pyrazinamide Not assoc w R - Interim
rpsA 1834354 c.813G>T synonymous_variant 0.33 pyrazinamide
rpsA 1834357 c.816T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834361 c.820T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.33 pyrazinamide Not assoc w R - Interim
rpsA 1834369 c.828C>G synonymous_variant 0.33 pyrazinamide
rpsA 1834378 c.837T>C synonymous_variant 0.37 pyrazinamide Not assoc w R - Interim
rpsA 1834387 c.846C>T synonymous_variant 0.36 pyrazinamide
rpsA 1834399 p.His286Gln missense_variant 0.33 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.31 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.31 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.31 pyrazinamide
rpsA 1834451 c.910_912delTTGinsCTC synonymous_variant 0.32 pyrazinamide
rpsA 1834456 c.915T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.3 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.3 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.27 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.27 pyrazinamide
rpsA 1834534 c.993C>G synonymous_variant 0.24 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.22 pyrazinamide
rpsA 1834543 c.1002C>G synonymous_variant 0.21 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834552 c.1011G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834555 c.1014T>G synonymous_variant 0.21 pyrazinamide
rpsA 1834557 p.Ala339Val missense_variant 0.21 pyrazinamide
rpsA 1834564 c.1023C>T synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
rpsA 1834591 c.1050C>T synonymous_variant 0.24 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.21 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.21 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568435 c.242_245delGTCCinsATCCTT frameshift_variant&missense_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3568442 p.Lys80Gln missense_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3568443 p.His79Gln missense_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3568854 c.-176delG upstream_gene_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3569220 c.-541C>T upstream_gene_variant 1.0 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 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
clpC1 4038905 c.1800A>G synonymous_variant 0.26 pyrazinamide
clpC1 4038911 c.1794G>T synonymous_variant 0.24 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.24 pyrazinamide
clpC1 4038917 c.1788C>T synonymous_variant 0.24 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.25 pyrazinamide
clpC1 4038932 c.1773G>C synonymous_variant 0.18 pyrazinamide
clpC1 4038941 c.1764G>C synonymous_variant 0.19 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.18 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038962 c.1743C>T synonymous_variant 0.17 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.17 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4038980 c.1725C>T synonymous_variant 0.17 pyrazinamide
clpC1 4038989 c.1716T>C synonymous_variant 0.18 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4039103 c.1602T>C synonymous_variant 0.29 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.28 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.29 pyrazinamide
clpC1 4039124 c.1581C>G synonymous_variant 0.29 pyrazinamide
clpC1 4039136 c.1569C>T synonymous_variant 0.3 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.27 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.27 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.22 pyrazinamide
clpC1 4039733 c.972G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039748 c.957G>C synonymous_variant 0.26 pyrazinamide
clpC1 4039751 c.954A>G synonymous_variant 0.26 pyrazinamide
clpC1 4039757 c.948A>G synonymous_variant 0.28 pyrazinamide
clpC1 4039766 c.939T>C synonymous_variant 0.33 pyrazinamide
clpC1 4039769 c.936C>G synonymous_variant 0.33 pyrazinamide
clpC1 4039778 c.927A>G synonymous_variant 0.31 pyrazinamide
clpC1 4039790 c.915C>T synonymous_variant 0.31 pyrazinamide
clpC1 4039793 c.912C>G synonymous_variant 0.32 pyrazinamide
clpC1 4039802 c.903G>C synonymous_variant 0.32 pyrazinamide
clpC1 4039817 c.888A>T synonymous_variant 0.39 pyrazinamide
clpC1 4039820 c.885T>G synonymous_variant 0.38 pyrazinamide
clpC1 4039831 c.874T>C synonymous_variant 0.39 pyrazinamide
clpC1 4039832 c.873C>G synonymous_variant 0.39 pyrazinamide
clpC1 4039835 c.870C>T synonymous_variant 0.39 pyrazinamide Not assoc w R - Interim
clpC1 4039850 c.855T>C synonymous_variant 0.38 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.32 pyrazinamide
clpC1 4039868 c.837C>T synonymous_variant 0.36 pyrazinamide Not assoc w R - Interim
clpC1 4039898 c.807C>G synonymous_variant 0.34 pyrazinamide
clpC1 4039913 c.792C>T synonymous_variant 0.26 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.28 pyrazinamide
clpC1 4039937 c.768G>C synonymous_variant 0.26 pyrazinamide
clpC1 4039943 c.762G>C synonymous_variant 0.26 pyrazinamide
clpC1 4039946 c.759A>T synonymous_variant 0.26 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.26 pyrazinamide
clpC1 4039955 c.750G>C synonymous_variant 0.28 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.21 pyrazinamide
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
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
ethA 4326513 p.Thr321Pro missense_variant 1.0 ethionamide Uncertain significance
ethA 4326676 p.Ser266Arg missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R