TB-Profiler result

Run: SRR5431730
Summary

Run ID: SRR5431730

Sample name:

Date: 2024-10-04T21:01:24.526623

Number of reads: 3608526

Percentage reads mapped: 74.36

Median coverage: 49.0

Strain: La1.8.1

Spoligotype:

Drug-resistance: Other

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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 0.99
La1 M.bovis None 0.99
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 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
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 0.99 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
gyrB 6811 c.1572C>T synonymous_variant 0.13 levofloxacin
moxifloxacin Not assoc w R - Interim
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 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
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
nusG 734841 c.588G>T synonymous_variant 0.13 rifampicin
nusG 734847 c.594T>C synonymous_variant 0.12 rifampicin
nusG 734853 c.600A>G synonymous_variant 0.12 rifampicin
nusG 734859 c.606G>C synonymous_variant 0.13 rifampicin
nusG 734863 p.Thr204Ser missense_variant 0.13 rifampicin
nusG 734895 c.642A>G synonymous_variant 0.16 rifampicin
rpoB 760283 c.477G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760649 c.843G>C synonymous_variant 0.16 rifampicin
rpoB 761015 c.1209G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.18 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761051 c.1245G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761201 c.1395G>A synonymous_variant 0.15 rifampicin
rpoB 761204 c.1398C>T synonymous_variant 0.16 rifampicin
rpoB 761207 c.1401C>T synonymous_variant 0.16 rifampicin
rpoB 761222 c.1416G>C synonymous_variant 0.15 rifampicin
rpoB 761240 c.1434C>T synonymous_variant 0.17 rifampicin
rpoB 761969 c.2163G>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761972 c.2166C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762006 c.2200_2202delCGCinsAGG synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762212 c.2406G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762995 c.3189G>T synonymous_variant 0.14 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 0.13 rifampicin Not assoc w R - Interim
rpoB 763094 c.3288G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763127 c.3321G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763142 c.-228C>G upstream_gene_variant 0.16 rifampicin
rpoC 763148 c.-222G>C upstream_gene_variant 0.17 rifampicin
rpoC 763169 c.-201A>G upstream_gene_variant 0.12 rifampicin
rpoC 763396 c.27A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763408 c.39T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763411 c.42T>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763414 c.45T>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763430 c.61A>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763444 c.75T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763447 c.78C>T synonymous_variant 0.14 rifampicin
rpoC 763594 c.225C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763618 c.249C>T synonymous_variant 0.2 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.14 rifampicin
rpoC 764085 p.Asn239Thr missense_variant 0.13 rifampicin Uncertain significance
rpoC 764087 p.Leu240Val missense_variant 0.15 rifampicin Uncertain significance
rpoC 764098 c.729A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764101 c.732C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764104 c.735C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764287 c.918C>T synonymous_variant 0.14 rifampicin
rpoC 764293 c.924G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764344 c.975C>T synonymous_variant 0.22 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>G synonymous_variant 0.13 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764863 c.1494G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764869 c.1500C>G synonymous_variant 0.17 rifampicin
rpoC 764875 c.1506C>T synonymous_variant 0.15 rifampicin
rpoC 764878 c.1509C>G synonymous_variant 0.18 rifampicin
rpoC 764887 c.1518G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.12 rifampicin
rpoC 764912 p.Met515Leu missense_variant 0.12 rifampicin
rpoC 764932 c.1563C>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765835 c.2466C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765871 c.2502T>C synonymous_variant 0.18 rifampicin
rpoC 765875 p.Val836Ile missense_variant 0.18 rifampicin Uncertain significance
rpoC 765886 c.2517C>G synonymous_variant 0.19 rifampicin
rpoC 765904 c.2535C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765908 c.2539C>T synonymous_variant 0.2 rifampicin
rpoC 765967 c.2598C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765973 c.2604C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766484 p.Val1039Ile missense_variant 0.19 rifampicin Uncertain significance
rpoC 767041 c.3672G>C synonymous_variant 0.22 rifampicin
rpoC 767044 c.3675G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
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
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 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472431 n.586G>A non_coding_transcript_exon_variant 0.18 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838_839insTA non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473100 n.1255G>C non_coding_transcript_exon_variant 0.21 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.2 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.21 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473111 n.1266A>T non_coding_transcript_exon_variant 0.22 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473123 n.1278A>T 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 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474715 n.1061delA non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476095 n.2438C>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1476103 n.2446C>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1476108 n.2451T>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476110 n.2453G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476246 n.2589G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476616 n.2959A>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476665 n.3008T>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476679 n.3022T>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
inhA 1673380 c.-822C>G upstream_gene_variant 0.24 isoniazid
ethionamide
rpsA 1833724 c.183C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833734 p.Ala65Ser missense_variant 0.16 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.16 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.18 pyrazinamide
rpsA 1833988 c.447C>G synonymous_variant 0.2 pyrazinamide
rpsA 1833991 c.450C>A synonymous_variant 0.18 pyrazinamide
rpsA 1834051 c.510G>A synonymous_variant 0.18 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834222 c.681T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834225 c.684C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834231 c.690T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
rpsA 1834456 c.915T>G synonymous_variant 0.15 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.17 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.16 pyrazinamide
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 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 0.98 pyrazinamide Uncertain significance
PPE35 2168319 p.Thr765Ile missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.33 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.32 pyrazinamide
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 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2517917 c.-198G>A upstream_gene_variant 0.93 isoniazid
kasA 2517926 c.-189G>A upstream_gene_variant 0.19 isoniazid
kasA 2517941 c.-174C>G upstream_gene_variant 0.12 isoniazid
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
eis 2715125 p.Thr70Ala missense_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
Rv2477c 2782927 c.1116A>G synonymous_variant 1.0 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R - Interim
Rv2680 2995832 c.-273G>A upstream_gene_variant 1.0 capreomycin
Rv2681 2997325 p.Ala196Val missense_variant 1.0 capreomycin 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
mtrB 3626996 c.-383G>C upstream_gene_variant 0.16 rifampicin
bedaquiline
mtrB 3627008 c.-395G>C upstream_gene_variant 0.16 rifampicin
bedaquiline
mtrB 3627011 c.-398T>G upstream_gene_variant 0.16 rifampicin
bedaquiline
fbiB 3641590 p.Gly19Glu missense_variant 0.97 pretomanid
delamanid Uncertain significance
clofazimine
rpoA 3877613 p.Ile299Val missense_variant 0.21 rifampicin
rpoA 3877617 c.891G>C synonymous_variant 0.22 rifampicin
rpoA 3877647 c.861C>T synonymous_variant 0.2 rifampicin
rpoA 3878247 c.261G>C synonymous_variant 0.19 rifampicin
rpoA 3878250 c.258C>G synonymous_variant 0.19 rifampicin
rpoA 3878253 c.255G>C synonymous_variant 0.2 rifampicin
rpoA 3878264 p.Ser82Gly missense_variant 0.17 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
clpC1 4038403 c.2302T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038640 p.Asp689Asn missense_variant 0.2 pyrazinamide
clpC1 4038647 c.2058T>G synonymous_variant 0.16 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4038704 c.2001T>C synonymous_variant 0.2 pyrazinamide
clpC1 4038710 c.1995G>C synonymous_variant 0.19 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038726 p.Thr660Ser missense_variant 0.15 pyrazinamide
clpC1 4038749 c.1956C>T synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4039889 c.816G>C synonymous_variant 0.12 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.17 pyrazinamide
clpC1 4039925 c.780C>T synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
clpC1 4039931 c.774T>C synonymous_variant 0.23 pyrazinamide
clpC1 4039934 c.771G>C synonymous_variant 0.24 pyrazinamide
clpC1 4039946 c.759A>T synonymous_variant 0.24 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.21 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.22 pyrazinamide
clpC1 4040021 c.684A>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4040024 c.681A>G synonymous_variant 0.14 pyrazinamide
clpC1 4040027 c.678C>G synonymous_variant 0.15 pyrazinamide
clpC1 4040030 c.675C>G synonymous_variant 0.15 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.16 pyrazinamide
clpC1 4040057 c.648C>T synonymous_variant 0.19 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
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
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
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