TB-Profiler result

Run: ERR3439489
Summary

Run ID: ERR3439489

Sample name:

Date: 2024-10-04T03:33:11.443234

Number of reads: 807185

Percentage reads mapped: 44.61

Median coverage: 23.0

Strain: La1.8.1

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
La1.8 M.bovis None 1.0
La1.8.1 M.bovis None 1.0
La1 M.bovis 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 p.Ser441Ala Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid
ethambutol
pyrazinamide pncA p.His57Asp Assoc w R
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
rpoB 761127 p.Ser441Ala missense_variant 0.26 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide 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
dnaA 467 p.His156Arg missense_variant 1.0 isoniazid Not assoc w R
gyrB 5752 c.513G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6406 c.1167C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
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 8285 c.984C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8741 c.1440C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9217 p.Asp639Ala missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13197 p.Thr121Ser missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 1.0 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
rpoB 761132 c.1326G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327_1329delTTGinsCTC synonymous_variant 0.28 rifampicin
rpoB 761150 c.1344A>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761153 c.1347G>C synonymous_variant 0.29 rifampicin
rpoB 761162 c.1356G>C synonymous_variant 0.26 rifampicin
rpoB 762863 c.3057T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 762879 p.Met1025Leu missense_variant 0.27 rifampicin Uncertain significance
rpoC 762896 c.-474G>C upstream_gene_variant 0.26 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 762932 c.-438G>C upstream_gene_variant 0.27 rifampicin
rpoC 762947 c.-423C>G upstream_gene_variant 0.32 rifampicin
rpoB 762962 c.3156C>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 762980 c.-390T>C upstream_gene_variant 0.28 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764662 c.1293G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764677 c.1308C>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764706 p.Leu446Gln missense_variant 0.43 rifampicin Uncertain significance
rpoC 764722 c.1353G>C synonymous_variant 0.41 rifampicin
rpoC 764740 p.Met457Ile missense_variant 0.36 rifampicin
rpoC 764746 c.1377G>C synonymous_variant 0.36 rifampicin
rpoC 764749 c.1380G>C synonymous_variant 0.35 rifampicin
rpoC 764750 p.Val461Ile missense_variant 0.35 rifampicin
rpoC 764758 c.1389C>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764760 p.Asn464Ser missense_variant 0.32 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764780 p.Ser471Ala missense_variant 0.29 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781802 c.243G>C synonymous_variant 0.38 streptomycin
rpsL 781817 c.258G>T synonymous_variant 0.37 streptomycin
rpsL 781829 c.270G>C synonymous_variant 0.35 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.35 streptomycin
rpsL 781835 c.276T>C synonymous_variant 0.36 streptomycin Not assoc w R - Interim
rplC 800648 c.-161A>G upstream_gene_variant 0.4 linezolid
rplC 800651 c.-158G>C upstream_gene_variant 0.4 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.43 linezolid
rplC 800667 c.-142_-140delTCGinsAGC upstream_gene_variant 0.46 linezolid
rplC 800672 c.-137G>C upstream_gene_variant 0.46 linezolid
rplC 800693 c.-116A>C upstream_gene_variant 0.5 linezolid
rplC 800702 c.-107G>T upstream_gene_variant 0.46 linezolid
rplC 800703 c.-106T>G upstream_gene_variant 0.46 linezolid
rplC 800715 c.-94_-92delATCinsGTG upstream_gene_variant 0.4 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.4 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.4 linezolid
rplC 800729 c.-80G>C upstream_gene_variant 0.38 linezolid
rplC 800733 c.-76A>G upstream_gene_variant 0.4 linezolid
rplC 800738 c.-71T>C upstream_gene_variant 0.4 linezolid
rplC 800742 c.-67G>T upstream_gene_variant 0.4 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
Rv1129c 1254582 c.-48A>G upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.69 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.65 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472582 n.737G>C non_coding_transcript_exon_variant 0.69 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.72 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.7 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.7 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472666 n.821G>A non_coding_transcript_exon_variant 0.7 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.68 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472674 n.829T>A non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.68 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472694 n.849C>T non_coding_transcript_exon_variant 0.65 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.68 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.46 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>G non_coding_transcript_exon_variant 0.46 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.46 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.46 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>T non_coding_transcript_exon_variant 0.46 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.81 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.85 kanamycin Uncertain significance
capreomycin
streptomycin
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.85 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.85 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473109 n.1264T>C non_coding_transcript_exon_variant 0.85 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.85 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.85 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.86 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.86 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.83 kanamycin Uncertain significance
capreomycin
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.77 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474675 n.1018C>A non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid
rrl 1474723 n.1066G>A non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474770 n.1113G>A non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.79 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474800 n.1143T>C non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475781 n.2124T>G non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.8 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.8 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.85 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.86 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid
rrl 1476544 n.2887T>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476566 n.2909A>T non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834859 p.Ala440Thr missense_variant 1.0 pyrazinamide Uncertain significance
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 2062922 p.Ile603Val missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2102193 p.Arg284Trp missense_variant 1.0 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
ndh 2103173 c.-132delG upstream_gene_variant 1.0 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 1.0 isoniazid Not assoc w R
katG 2156025 c.87C>A synonymous_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168011 p.Ser868Arg missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
eis 2715125 p.Thr70Ala missense_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
Rv2681 2997325 p.Ala196Val missense_variant 1.0 capreomycin Uncertain significance
Rv2752c 3065988 p.Glu68Asp missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086728 c.-92C>T upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
Rv3083 3448783 p.Val94Ile missense_variant 1.0 ethionamide Uncertain significance
lpqB 3623372 c.1539G>C synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3623730 p.Ser394Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624593 c.318G>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624710 c.201G>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038403 c.2302T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4039979 c.726C>G synonymous_variant 0.37 pyrazinamide
clpC1 4040000 p.His235Lys missense_variant 0.44 pyrazinamide
clpC1 4040003 c.702G>C synonymous_variant 0.44 pyrazinamide
clpC1 4040009 c.696C>G synonymous_variant 0.44 pyrazinamide
clpC1 4040018 c.687G>C synonymous_variant 0.41 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.4 pyrazinamide Not assoc w R - Interim
clpC1 4040024 c.681A>G synonymous_variant 0.4 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.41 pyrazinamide
clpC1 4040063 c.642G>C synonymous_variant 0.35 pyrazinamide Not assoc w R - Interim
clpC1 4040066 c.639G>C synonymous_variant 0.36 pyrazinamide
clpC1 4040069 c.636G>C synonymous_variant 0.36 pyrazinamide
clpC1 4040083 p.Thr208Ser missense_variant 0.38 pyrazinamide
clpC1 4040087 c.618G>C synonymous_variant 0.38 pyrazinamide
clpC1 4040090 c.615T>C synonymous_variant 0.38 pyrazinamide Not assoc w R - Interim
clpC1 4040096 p.Val203Ile missense_variant 0.38 pyrazinamide
clpC1 4040117 c.588A>G synonymous_variant 0.29 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4138977 p.Gly260Ala missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242970 c.3108C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242981 p.Met1040Thr missense_variant 1.0 ethambutol Uncertain significance
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246551 p.Asn13Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
aftB 4267858 p.Ile327Val missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R