TB-Profiler result

Run: ERR4800102
Summary

Run ID: ERR4800102

Sample name:

Date: 2024-10-04T16:27:28.479080

Number of reads: 3535414

Percentage reads mapped: 82.62

Median coverage: 103.0

Strain: lineage3.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.99
lineage3.1.2 East-African-Indian RD750 0.83
lineage3.1.2.1 East-African-Indian RD750 0.84
lineage3.1 East-African-Indian RD750 0.89
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
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
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 9017 c.1716C>G synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 620698 p.Val270Ile missense_variant 0.13 kanamycin
capreomycin
amikacin
Rv0565c 657081 c.390G>A synonymous_variant 0.99 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 760991 c.1185G>C synonymous_variant 0.14 rifampicin
rpoB 760997 c.1191G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761006 c.1200C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761027 c.1221A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761051 c.1245G>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761063 c.1257C>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.26 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.29 rifampicin
rpoB 761132 c.1326G>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761160 c.1354C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761189 c.1383T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761198 c.1392G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761217 p.Pro471Ala missense_variant 0.12 rifampicin
rpoB 761220 p.Ser472Thr missense_variant 0.12 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>C synonymous_variant 0.16 rifampicin
rpoB 761261 c.1455G>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761813 c.2007T>C synonymous_variant 0.14 rifampicin
rpoB 761834 c.2028T>G synonymous_variant 0.13 rifampicin
rpoB 761847 p.Cys681Arg missense_variant 0.12 rifampicin Uncertain significance
rpoB 761862 p.Ala686Ser missense_variant 0.12 rifampicin
rpoB 761868 p.Asp688His missense_variant 0.12 rifampicin
rpoB 761873 c.2067A>G synonymous_variant 0.12 rifampicin
rpoB 762065 c.2259T>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762068 c.2262C>T synonymous_variant 0.12 rifampicin
rpoB 762185 c.2379G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762209 c.2403C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762218 c.2412T>C synonymous_variant 0.19 rifampicin
rpoB 762224 c.2418C>G synonymous_variant 0.21 rifampicin
rpoB 762233 c.2427G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762245 c.2439G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762254 c.2448T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762266 c.2460T>C synonymous_variant 0.15 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 762983 c.-387C>T upstream_gene_variant 0.13 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763028 c.3222T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763052 c.-318G>C upstream_gene_variant 0.18 rifampicin
rpoC 763058 c.-312C>G upstream_gene_variant 0.18 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763094 c.3288G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764257 c.888G>C synonymous_variant 0.12 rifampicin
rpoC 764284 c.915G>C synonymous_variant 0.12 rifampicin
rpoC 764297 p.Met310Leu missense_variant 0.12 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.18 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764701 c.1332C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764923 c.1554A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764935 c.1566T>C synonymous_variant 0.13 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764953 c.1584G>C synonymous_variant 0.17 rifampicin
rpoC 764956 c.1587T>C synonymous_variant 0.16 rifampicin
rpoC 764968 c.1599T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764971 c.1602C>G synonymous_variant 0.17 rifampicin
rpoC 765004 c.1635G>T synonymous_variant 0.13 rifampicin
rpoC 765007 c.1638T>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765008 c.1639T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765016 c.1647C>G synonymous_variant 0.13 rifampicin
rpoC 765019 c.1650A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766933 c.3564A>G synonymous_variant 0.12 rifampicin
rpoC 766942 c.3573C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766945 c.3576A>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766948 c.3579G>C synonymous_variant 0.13 rifampicin
rpoC 766957 c.3588G>A synonymous_variant 0.13 rifampicin
rpoC 766960 c.3591C>T synonymous_variant 0.13 rifampicin
rpoC 766963 c.3594T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.12 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775961 c.2520C>G synonymous_variant 0.12 bedaquiline
clofazimine
mmpL5 775981 p.Leu834Met missense_variant 0.14 bedaquiline
clofazimine
mmpL5 775991 c.2490G>A synonymous_variant 0.12 bedaquiline
clofazimine
mmpL5 775997 c.2484T>C synonymous_variant 0.13 bedaquiline
clofazimine
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 781817 c.258G>T synonymous_variant 0.16 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.14 streptomycin Uncertain significance
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472027 n.182C>T non_coding_transcript_exon_variant 0.21 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472032 n.187G>C non_coding_transcript_exon_variant 0.21 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472033 n.188A>C non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472040 n.195T>G non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472041 n.196C>G non_coding_transcript_exon_variant 0.22 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472279 n.434T>C non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472289 n.444T>C non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472290 n.445C>A non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472297 n.453_465delGTCCGGGTTCTCT non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472313 n.468delGinsCA non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472324 n.479G>T non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.23 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.34 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.25 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTC non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445delCinsTT non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1473768 n.111A>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1473823 n.166T>C non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473887 n.230T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474629 n.972G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474640 n.983C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475375 n.1718G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475376 n.1719A>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid Uncertain significance
rrl 1475379 n.1722G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475398 n.1741C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475403 n.1746T>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475404 n.1747A>C non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475405 n.1748A>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475408 n.1752delT non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475430 n.1773T>G non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1475482 n.1825A>T non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1475483 n.1826C>A non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1475759 n.2102C>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475762 n.2105delGinsTTT non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475764 n.2107A>G non_coding_transcript_exon_variant 0.24 capreomycin
linezolid Uncertain significance
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.24 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475989 n.2332T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.19 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476664 n.3007T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1476665 n.3008T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476679 n.3022T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476689 n.3033delC non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1476693 n.3036delGinsCAA non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
inhA 1674801 c.600T>C synonymous_variant 0.13 isoniazid
ethionamide
inhA 1674870 c.669T>C synonymous_variant 0.12 isoniazid
ethionamide
rpsA 1833862 c.321G>T synonymous_variant 0.13 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.13 pyrazinamide
rpsA 1833904 c.363G>A synonymous_variant 0.12 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833955 c.414G>C synonymous_variant 0.12 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.17 pyrazinamide
rpsA 1833988 c.447C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833991 c.450C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834009 c.468C>G synonymous_variant 0.17 pyrazinamide
rpsA 1834012 c.471G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.17 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.17 pyrazinamide
rpsA 1834040 p.Lys167Arg missense_variant 0.15 pyrazinamide
rpsA 1834054 c.513C>G synonymous_variant 0.19 pyrazinamide
rpsA 1834090 c.549G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834096 c.555G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834102 c.561T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834114 c.573G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834357 c.816T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834361 c.820T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
rpsA 1834396 c.855G>C synonymous_variant 0.2 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.19 pyrazinamide
rpsA 1834432 c.891G>C synonymous_variant 0.2 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834456 c.915T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.2 pyrazinamide
rpsA 1834474 c.933C>T synonymous_variant 0.18 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834504 c.963G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834520 p.Ala327Ser missense_variant 0.15 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834543 c.1002C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834554 c.1014_1015delTG frameshift_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834558 c.1017_1018insAG frameshift_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834603 p.Glu354Asp missense_variant 0.12 pyrazinamide
rpsA 1834606 c.1065C>T synonymous_variant 0.13 pyrazinamide
rpsA 1834612 c.1071G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834622 p.Ser361Thr missense_variant 0.12 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.14 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
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.86 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 2289047 c.195C>T synonymous_variant 0.99 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.98 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.96 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2680 2996097 c.-8A>C upstream_gene_variant 0.4 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877848 c.660C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3877856 c.652T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.14 rifampicin
rpoA 3877875 c.633T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877881 c.627G>C synonymous_variant 0.14 rifampicin
rpoA 3877887 c.621G>C synonymous_variant 0.15 rifampicin
rpoA 3877893 c.615C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877905 c.603A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877908 c.600T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877920 c.588G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877926 c.582G>C synonymous_variant 0.15 rifampicin
clpC1 4038878 c.1827A>G synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
clpC1 4039001 p.Asn568Lys missense_variant 0.12 pyrazinamide
clpC1 4039064 c.1641C>T synonymous_variant 0.13 pyrazinamide
clpC1 4039067 c.1638G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039073 c.1632C>T synonymous_variant 0.12 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.14 pyrazinamide
clpC1 4039526 c.1179G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039550 c.1155G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039559 c.1146C>G synonymous_variant 0.14 pyrazinamide
clpC1 4039565 c.1140G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039570 p.Met379Leu missense_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039576 p.Ala377Pro missense_variant 0.13 pyrazinamide
clpC1 4039589 c.1116G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039592 c.1113G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039610 c.1095G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039613 c.1092C>T synonymous_variant 0.15 pyrazinamide
clpC1 4039622 c.1083C>T synonymous_variant 0.16 pyrazinamide
clpC1 4039649 c.1056G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039652 c.1053G>C synonymous_variant 0.17 pyrazinamide
clpC1 4039661 c.1044T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039688 c.1017G>A synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4039724 c.981A>G synonymous_variant 0.13 pyrazinamide
clpC1 4039733 c.972G>T synonymous_variant 0.11 pyrazinamide
clpC1 4039751 c.954A>G synonymous_variant 0.12 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R