TB-Profiler result

Run: ERR751345
Summary

Run ID: ERR751345

Sample name:

Date: 2024-10-05T00:41:45.944081

Number of reads: 3876190

Percentage reads mapped: 82.13

Median coverage: 83.0

Strain: lineage5.1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage5.1.1 West-Africa 1 RD711 1.0
lineage5 West-Africa 1 RD711 1.0
lineage5.1 West-Africa 1 RD711 0.88
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin rrs n.799C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance Mutation from literature
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.34 amikacin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.27 amikacin Assoc w R
capreomycin Assoc w R
kanamycin 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 782 p.Ser261Thr missense_variant 1.0 isoniazid Uncertain significance
gyrB 5150 c.-89delC upstream_gene_variant 0.99 levofloxacin
moxifloxacin
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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_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
gyrA 9566 c.2265C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
Rv0010c 13579 c.-21G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
hadA 731750 c.-180G>C upstream_gene_variant 1.0 isoniazid
rpoB 761015 c.1209G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761027 c.1221A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231_1233delTTGinsCTC synonymous_variant 0.18 rifampicin
rpoB 761064 p.Ala420Ser missense_variant 0.22 rifampicin Uncertain significance
rpoB 761096 c.1290G>C synonymous_variant 0.22 rifampicin
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.22 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.22 rifampicin
rpoB 762002 c.2196C>G synonymous_variant 0.14 rifampicin
rpoB 762003 p.Asn733Gln missense_variant 0.14 rifampicin
rpoB 762011 c.2205G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762015 p.Glu737Gln missense_variant 0.14 rifampicin
rpoB 762020 p.Glu738Asp missense_variant 0.14 rifampicin
rpoB 762026 c.2220G>C synonymous_variant 0.16 rifampicin
rpoB 762030 p.Thr742Ser missense_variant 0.15 rifampicin
rpoB 762053 c.2247T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762057 p.Ile751Val missense_variant 0.13 rifampicin Uncertain significance
rpoB 762917 c.3111C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763280 c.3474C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 763501 p.Asp44Glu missense_variant 0.11 rifampicin Uncertain significance
rpoC 763507 c.138G>C synonymous_variant 0.11 rifampicin
rpoC 763517 p.Lys50Arg missense_variant 0.1 rifampicin
rpoC 763537 c.168C>G synonymous_variant 0.1 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763551 p.Tyr61Ser missense_variant 0.12 rifampicin
rpoC 763573 c.204G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763621 c.252C>G synonymous_variant 0.12 rifampicin
rpoC 763624 c.255C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763625 p.Lys86Gly missense_variant 0.12 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.1 rifampicin
rpoC 764602 c.1233C>G synonymous_variant 0.13 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764620 c.1251G>C synonymous_variant 0.14 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764644 c.1275G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764701 c.1332C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764705 p.Leu446Ala missense_variant 0.16 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764722 c.1353G>C synonymous_variant 0.18 rifampicin
rpoC 764731 c.1362G>C synonymous_variant 0.17 rifampicin
rpoC 764737 c.1368G>C synonymous_variant 0.15 rifampicin
rpoC 764749 c.1380G>C synonymous_variant 0.14 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
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 1302899 c.-32A>G upstream_gene_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv1258c 1407273 p.Asp23Val missense_variant 0.99 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.58 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472583 n.738T>C non_coding_transcript_exon_variant 0.45 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.29 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 0.3 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473127 n.1282G>A non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.35 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.26 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473320 n.1475G>A non_coding_transcript_exon_variant 0.24 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474166 n.509G>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474179 n.522C>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474202 n.545T>A non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474636 n.979_982delACCGinsTTAC non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1474660 n.1003G>A non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474690 n.1033C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060_1061insGTGAG non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.77 capreomycin Not assoc w R
linezolid Uncertain significance
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 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475752 n.2095C>G non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475762 n.2105_2106delGCinsT non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475776 n.2119G>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.36 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475991 n.2334T>A non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1475996 n.2339T>G non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476179 n.2522C>T non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.45 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.46 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 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476226 n.2569G>A non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.26 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476422 n.2765C>G non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.5 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid
rrl 1476431 n.2774G>C non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476544 n.2887T>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1476566 n.2909A>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673338 c.-864G>A upstream_gene_variant 1.0 isoniazid
ethionamide
inhA 1674769 p.Ala190Ser missense_variant 0.99 isoniazid Uncertain significance
ethionamide Uncertain significance
rpsA 1833697 c.156C>G synonymous_variant 0.11 pyrazinamide
rpsA 1833721 c.180A>G synonymous_variant 0.13 pyrazinamide
rpsA 1833724 c.183C>T synonymous_variant 0.14 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833985 c.444G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833994 c.453G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833997 c.456G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834009 c.468C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834012 c.471G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834024 c.483G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.18 pyrazinamide
rpsA 1834034 p.Ile165Val missense_variant 0.2 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834090 c.549G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834093 c.552G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.12 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
rpsA 1834286 p.Ser249Gly missense_variant 0.11 pyrazinamide
rpsA 1834294 c.753G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834298 p.Gln253Glu missense_variant 0.12 pyrazinamide
rpsA 1834303 c.762T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834327 c.786G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834354 c.813G>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
rpsA 1834357 c.816T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834360 c.819G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834361 c.820T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.11 pyrazinamide Not assoc w R - Interim
rpsA 1834378 c.837T>G synonymous_variant 0.13 pyrazinamide
rpsA 1834384 c.843A>G synonymous_variant 0.13 pyrazinamide
rpsA 1834395 p.Arg285Gln missense_variant 0.13 pyrazinamide
rpsA 1834408 c.867C>G synonymous_variant 0.12 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834423 c.882G>T synonymous_variant 0.13 pyrazinamide
rpsA 1834427 p.Ile296Val missense_variant 0.12 pyrazinamide Uncertain significance
rpsA 1834451 c.910_912delTTGinsCTC synonymous_variant 0.15 pyrazinamide
rpsA 1834456 c.915T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834459 c.918G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.17 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.18 pyrazinamide
rpsA 1834486 p.Glu315Asp missense_variant 0.13 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834501 c.960G>C synonymous_variant 0.12 pyrazinamide
tsnR 1853565 c.-41G>A upstream_gene_variant 1.0 linezolid 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 2101773 p.Thr424Pro missense_variant 0.98 isoniazid Uncertain significance
delamanid
ethionamide Uncertain significance
ndh 2101921 c.1122G>A synonymous_variant 0.99 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
ndh 2103112 c.-70G>T upstream_gene_variant 1.0 isoniazid Not assoc w R - Interim
delamanid Uncertain significance
ethionamide Uncertain significance
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
pncA 2290062 c.-821G>A upstream_gene_variant 1.0 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
Rv2477c 2784160 c.-527_-119del upstream_gene_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0 cycloserine
Rv3083 3449004 c.502_504delCAC conservative_inframe_deletion 1.0 ethionamide
Rv3083 3449644 p.Ala381Thr missense_variant 0.99 ethionamide 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
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840932 c.489C>T synonymous_variant 1.0 cycloserine
rpoA 3878493 c.15G>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
ddn 3986987 c.144G>T synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
ddn 3987180 p.Asp113Asn missense_variant 1.0 pretomanid
delamanid Uncertain significance
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0 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 4139131 p.Glu209Lys missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Not assoc w R
ethambutol Uncertain significance
glpK 4139183 c.572dupG frameshift_variant 0.67 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4239843 c.-20A>C upstream_gene_variant 1.0 ethambutol Not assoc w R - Interim
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
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244635 p.Val468Ala missense_variant 1.0 ethambutol Not assoc w R - Interim
embA 4245147 p.Pro639Ser missense_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_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
ubiA 4269630 c.204G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
ethA 4326928 c.546C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethA 4327103 p.Gly124Asp 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 4407748 p.Leu152Ser missense_variant 1.0 streptomycin Uncertain significance