TB-Profiler result

Run: ERR550637
Summary

Run ID: ERR550637

Sample name:

Date: 2024-04-16T02:40:05.429917

Number of reads: 637725

Percentage reads mapped: 78.44

Median coverage: 19.0

Strain: lineage4.1.1.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.97
lineage4.1.1.3 Euro-American (X-type) RD193 0.98
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) 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 rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>G Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Arg154Gly Assoc w R
streptomycin rrs n.878G>A Assoc w R - Interim
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine ald c.464delG Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.1192_1194dupGTG Mutation from literature
c.869dupA Assoc w R
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 761155 p.Ser450Leu missense_variant 0.73 rifampicin Assoc w R
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.79 streptomycin Assoc w R - Interim
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288782 p.Arg154Gly missense_variant 1.0 pyrazinamide Assoc w R
ald 3087278 c.464delG frameshift_variant 1.0 cycloserine Mutation from literature
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.77 ethambutol Assoc w R
ethA 4326279 c.1192_1194dupGTG conservative_inframe_insertion 0.97 ethionamide Mutation from literature
ethA 4326604 c.869dupA frameshift_variant 1.0 ethionamide 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 1161 c.1161A>G synonymous_variant 0.2 isoniazid
dnaA 1383 c.1383A>G synonymous_variant 0.18 isoniazid
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 8453 c.1152A>C synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 8459 c.1158G>A synonymous_variant 0.21 levofloxacin
moxifloxacin
gyrA 8462 c.1161A>C synonymous_variant 0.21 levofloxacin
moxifloxacin
gyrA 8465 c.1164C>G synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 8471 c.1170T>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8472 c.1171C>T synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8480 c.1179C>T synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8486 c.1185T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8513 c.1212C>G synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8516 c.1215T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8519 c.1218A>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760591 p.Val262Ala missense_variant 0.3 rifampicin
rpoB 760611 c.805T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 760655 c.849A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.33 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 760718 c.912C>G synonymous_variant 0.23 rifampicin
rpoB 760919 c.1113C>G synonymous_variant 0.25 rifampicin
rpoB 760925 c.1119T>C synonymous_variant 0.25 rifampicin
rpoB 760946 c.1140A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 760973 c.1167G>C synonymous_variant 0.24 rifampicin
rpoB 760982 c.1176G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761006 c.1200C>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.33 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 761129 c.1323G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 761189 c.1383T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761234 c.1428G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 761264 c.1458C>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761300 c.1494G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 761318 c.1512G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762131 c.2325C>G synonymous_variant 0.29 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.3 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 762266 c.2460T>C synonymous_variant 0.28 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 762285 p.Arg827Cys missense_variant 0.68 rifampicin Uncertain significance
rpoB 762293 c.2487T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 762296 c.2490G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 762317 c.2511A>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 762329 c.2523G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 762338 c.2532T>C synonymous_variant 0.32 rifampicin
rpoB 762347 c.2541T>C synonymous_variant 0.29 rifampicin
rpoC 762398 c.-972T>C upstream_gene_variant 0.32 rifampicin
rpoC 762407 c.-963G>A upstream_gene_variant 0.27 rifampicin
rpoC 762410 c.-960T>C upstream_gene_variant 0.27 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 762827 c.3021G>C synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 763139 c.-231C>T upstream_gene_variant 0.42 rifampicin
rpoC 763486 c.117T>G synonymous_variant 0.25 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>T synonymous_variant 0.19 rifampicin
rpoC 763573 c.204G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763576 c.207C>G synonymous_variant 0.21 rifampicin
rpoC 763594 c.225C>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763624 c.255C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763765 c.396T>C synonymous_variant 0.21 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.21 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765466 c.2097C>T synonymous_variant 0.28 rifampicin
rpoC 765478 c.2109T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 765508 c.2139C>G synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 765529 c.2160C>T synonymous_variant 0.32 rifampicin
rpoC 765541 c.2172C>G synonymous_variant 0.29 rifampicin
rpoC 765553 c.2184C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 765556 c.2187G>C synonymous_variant 0.29 rifampicin
rpoC 765583 c.2214G>C synonymous_variant 0.22 rifampicin
rpoC 765734 c.2365T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.22 rifampicin
rpoC 765826 c.2457T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 765886 c.2517C>G synonymous_variant 0.27 rifampicin
rpoC 766021 c.2652G>C synonymous_variant 0.2 rifampicin
rpoC 766027 c.2658G>C synonymous_variant 0.2 rifampicin
rpoC 766426 c.3057C>T synonymous_variant 0.33 rifampicin
rpoC 766447 c.3078T>C synonymous_variant 0.27 rifampicin
rpoC 766462 c.3093G>T synonymous_variant 0.23 rifampicin
rpoC 766483 c.3114G>C synonymous_variant 0.22 rifampicin
rpoC 766484 c.3115_3117delGTAinsAC frameshift_variant&missense_variant 0.23 rifampicin
rpoC 766492 c.3123T>C synonymous_variant 0.23 rifampicin
rpoC 766495 c.3126C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 766693 c.3324C>T synonymous_variant 0.21 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.18 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.23 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.25 rifampicin
rpoC 766801 c.3432C>A synonymous_variant 0.32 rifampicin
rpoC 766978 c.3609C>A synonymous_variant 0.27 rifampicin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781435 c.-125G>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781832 c.273T>C synonymous_variant 0.28 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.25 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.28 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.27 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.28 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.31 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.27 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.3 streptomycin
rplC 800219 c.-590T>C upstream_gene_variant 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472044 n.199G>T non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.2 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1473831 n.174G>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473966 n.309T>C non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1473971 n.314G>T non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1473981 n.324delGinsTT non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.33 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1474036 n.379G>A non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1474054 n.397T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.33 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 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1474961 n.1304T>G non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474963 n.1306G>A non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474964 n.1307T>C non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475409 n.1752T>C non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475446 n.1789G>A non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.24 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 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.17 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid
rpsA 1833589 c.48A>T synonymous_variant 0.31 pyrazinamide
rpsA 1833595 c.54T>G synonymous_variant 0.31 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.35 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.29 pyrazinamide
rpsA 1833760 c.219C>T synonymous_variant 0.29 pyrazinamide Not assoc w R - Interim
rpsA 1833793 c.252C>T synonymous_variant 0.33 pyrazinamide
rpsA 1833799 c.258C>G synonymous_variant 0.39 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.38 pyrazinamide
rpsA 1833835 c.294C>T synonymous_variant 0.35 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.37 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.35 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.38 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.36 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.27 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.27 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.24 pyrazinamide
tsnR 1853361 c.-245T>C upstream_gene_variant 0.38 linezolid
tsnR 1853370 c.-236_-234delGCAinsTG upstream_gene_variant 0.4 linezolid
tsnR 1853387 c.-219T>G upstream_gene_variant 0.46 linezolid
tsnR 1853394 c.-212_-211delCTinsGC upstream_gene_variant 0.4 linezolid
tsnR 1853420 c.-186T>G upstream_gene_variant 0.35 linezolid
tsnR 1853429 c.-177G>C upstream_gene_variant 0.33 linezolid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
rpoA 3878082 c.426T>C synonymous_variant 0.27 rifampicin
rpoA 3878094 c.414C>G synonymous_variant 0.27 rifampicin
rpoA 3878103 c.405A>G synonymous_variant 0.27 rifampicin
rpoA 3878106 c.402G>C synonymous_variant 0.27 rifampicin
rpoA 3878118 c.390T>C synonymous_variant 0.3 rifampicin
rpoA 3878141 p.Met123Leu missense_variant 0.35 rifampicin Uncertain significance
rpoA 3878143 p.Gly122Asp missense_variant 0.35 rifampicin Uncertain significance
rpoA 3878163 c.345C>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoA 3878169 c.339G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3878193 c.315T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoA 3878205 c.303T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoA 3878247 c.261G>C synonymous_variant 0.42 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3878276 c.232C>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3878284 p.Glu75Ala missense_variant 0.35 rifampicin
rpoA 3878292 c.216T>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3878298 c.210A>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>T synonymous_variant 0.35 rifampicin
rpoA 3878313 c.195G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
clpC1 4038623 c.2082A>G synonymous_variant 0.32 pyrazinamide
clpC1 4038640 p.Asp689Asn missense_variant 0.31 pyrazinamide
clpC1 4038653 c.2052C>T synonymous_variant 0.29 pyrazinamide
clpC1 4038671 c.2034T>C synonymous_variant 0.3 pyrazinamide
clpC1 4038677 c.2028G>T synonymous_variant 0.28 pyrazinamide
clpC1 4038683 c.2022T>G synonymous_variant 0.27 pyrazinamide
clpC1 4038695 c.2010C>G synonymous_variant 0.24 pyrazinamide
clpC1 4038701 c.2004G>C synonymous_variant 0.21 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 0.21 pyrazinamide
clpC1 4038707 c.1998C>G synonymous_variant 0.21 pyrazinamide
clpC1 4038710 c.1995G>C synonymous_variant 0.21 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.21 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 0.27 pyrazinamide
clpC1 4038755 c.1950G>T synonymous_variant 0.27 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.23 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.2 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.28 pyrazinamide
clpC1 4038815 c.1890G>C synonymous_variant 0.27 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.61 pyrazinamide Not assoc w R - Interim
clpC1 4038977 c.1728G>C synonymous_variant 0.38 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.36 pyrazinamide Not assoc w R - Interim
clpC1 4039022 c.1683A>G synonymous_variant 0.25 pyrazinamide
clpC1 4039034 c.1671C>G synonymous_variant 0.24 pyrazinamide
clpC1 4039661 c.1044T>C synonymous_variant 0.25 pyrazinamide
clpC1 4039670 c.1035G>C synonymous_variant 0.24 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.21 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.31 pyrazinamide
clpC1 4039946 c.759A>T synonymous_variant 0.25 pyrazinamide
clpC1 4039979 c.726C>G synonymous_variant 0.22 pyrazinamide
clpC1 4039991 c.714G>T synonymous_variant 0.2 pyrazinamide
clpC1 4039996 p.Glu237Gln missense_variant 0.21 pyrazinamide
clpC1 4040171 c.534C>G synonymous_variant 0.24 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4247485 c.972C>T synonymous_variant 0.31 ethambutol
embB 4247512 c.999T>C synonymous_variant 0.37 ethambutol
embB 4247544 p.Ser344Thr missense_variant 0.32 ethambutol
embB 4247554 c.1041T>C synonymous_variant 0.35 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407798 c.405G>T synonymous_variant 1.0 streptomycin Not assoc w R