TB-Profiler result

Run: SRR13861400
Summary

Run ID: SRR13861400

Sample name:

Date: 2024-10-05T10:19:31.193451

Number of reads: 1561918

Percentage reads mapped: 52.11

Median coverage: 52.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 0.98
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.888G>A Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fbiC c.1301delC Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1304229 c.1301delC frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance Mutation from literature
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 636 c.636C>G synonymous_variant 0.16 isoniazid
dnaA 645 c.645A>G synonymous_variant 0.21 isoniazid Not assoc w R - Interim
dnaA 654 c.654A>G synonymous_variant 0.21 isoniazid
dnaA 660 c.660G>C synonymous_variant 0.19 isoniazid Not assoc w R - Interim
dnaA 663 c.663A>C synonymous_variant 0.19 isoniazid
dnaA 669 c.669C>T synonymous_variant 0.19 isoniazid
dnaA 672 c.672T>C synonymous_variant 0.19 isoniazid Not assoc w R - Interim
dnaA 675 c.675C>G synonymous_variant 0.18 isoniazid Not assoc w R - Interim
dnaA 682 c.682_684delTTGinsCTC synonymous_variant 0.16 isoniazid
dnaA 690 c.690G>C synonymous_variant 0.17 isoniazid
dnaA 693 c.693A>C synonymous_variant 0.18 isoniazid
dnaA 705 c.705A>G synonymous_variant 0.15 isoniazid
dnaA 729 c.729C>G synonymous_variant 0.2 isoniazid Not assoc w R - Interim
dnaA 741 c.741T>C synonymous_variant 0.17 isoniazid Not assoc w R - Interim
dnaA 750 c.750C>G synonymous_variant 0.2 isoniazid
dnaA 756 c.756T>C synonymous_variant 0.21 isoniazid
dnaA 771 c.771A>C synonymous_variant 0.24 isoniazid
dnaA 777 c.777A>G synonymous_variant 0.22 isoniazid
dnaA 786 c.786C>T synonymous_variant 0.19 isoniazid
dnaA 795 c.795A>C synonymous_variant 0.15 isoniazid Not assoc w R - Interim
dnaA 804 c.804G>C synonymous_variant 0.17 isoniazid
dnaA 805 c.805T>C synonymous_variant 0.18 isoniazid
dnaA 813 c.813C>T synonymous_variant 0.18 isoniazid
dnaA 828 c.828T>C synonymous_variant 0.18 isoniazid Not assoc w R - Interim
dnaA 831 c.831A>G synonymous_variant 0.17 isoniazid
dnaA 837 c.837A>G synonymous_variant 0.17 isoniazid
dnaA 840 c.840G>A synonymous_variant 0.17 isoniazid
dnaA 843 c.843T>C synonymous_variant 0.16 isoniazid Not assoc w R - Interim
dnaA 846 c.846T>C synonymous_variant 0.16 isoniazid
dnaA 849 c.849A>G synonymous_variant 0.16 isoniazid
dnaA 1110 c.1110T>C synonymous_variant 0.14 isoniazid
dnaA 1125 c.1125G>C synonymous_variant 0.15 isoniazid
dnaA 1152 c.1152A>G synonymous_variant 0.16 isoniazid
dnaA 1153 c.1153T>C synonymous_variant 0.16 isoniazid
gyrA 7697 c.396C>G synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7760 c.459C>T synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7763 c.462T>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7799 c.498A>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7835 c.534A>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7838 c.537C>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8399 c.1098T>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8597 c.1296C>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8603 c.1302A>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8619 c.1318T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8672 c.1371A>G synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8693 c.1392T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8699 c.1398A>G synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8711 c.1410A>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8714 c.1413A>G synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8717 c.1416C>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8720 c.1419G>A synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8729 c.1428T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8732 c.1431G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8765 p.Asp488Glu missense_variant 0.16 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8880 p.Lys527Gln missense_variant 0.94 levofloxacin
moxifloxacin
mshA 575713 c.366G>A synonymous_variant 0.13 isoniazid
ethionamide
mshA 575719 c.372C>T synonymous_variant 0.13 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
mshA 575752 c.405G>A synonymous_variant 0.12 isoniazid Not assoc w R - Interim
ethionamide
nusG 734475 c.222T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
nusG 734481 c.228C>G synonymous_variant 0.13 rifampicin
mmaA3 737817 c.333A>G synonymous_variant 1.0 isoniazid
rpoB 760181 c.375T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.15 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760307 c.501T>C synonymous_variant 0.16 rifampicin
rpoB 760328 c.522G>C synonymous_variant 0.15 rifampicin
rpoB 760337 c.531C>G synonymous_variant 0.16 rifampicin
rpoB 760340 c.534G>C synonymous_variant 0.16 rifampicin
rpoB 760361 c.555T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760406 c.600G>C synonymous_variant 0.16 rifampicin
rpoB 760418 c.612G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760424 c.618C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760514 c.708C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760533 p.Val243Thr missense_variant 0.13 rifampicin
rpoB 760547 c.741G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760972 p.Arg389Leu missense_variant 0.9 rifampicin
rpoB 762218 c.2412T>G synonymous_variant 0.14 rifampicin
rpoB 762254 c.2448T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762266 c.2460T>C synonymous_variant 0.16 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762293 c.2487T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762317 c.2511A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762329 c.2523G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762338 c.2532T>C synonymous_variant 0.14 rifampicin
rpoC 763945 c.576T>C synonymous_variant 0.14 rifampicin
rpoC 763960 c.591T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763967 p.Gly200Ser missense_variant 0.15 rifampicin
rpoC 765111 p.Met581Lys missense_variant 0.96 rifampicin
rpoC 765161 p.Glu598Lys missense_variant 1.0 rifampicin
rpoC 765404 p.Leu679Val missense_variant 0.15 rifampicin
rpoC 765540 p.Ala724Val missense_variant 0.88 rifampicin
rpoC 766483 c.3114G>C synonymous_variant 0.14 rifampicin
rpoC 766486 c.3117A>C synonymous_variant 0.14 rifampicin
rpoC 766495 c.3126C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 767068 c.3699G>T synonymous_variant 0.94 rifampicin
mmpR5 778439 c.-551C>A upstream_gene_variant 1.0 bedaquiline
clofazimine
rplC 801357 p.His183Gln missense_variant 1.0 linezolid
rrs 1472044 n.199G>C non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.16 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 1472106 n.261G>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.33 kanamycin
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.23 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.16 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472288 n.444delT non_coding_transcript_exon_variant 0.89 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.27 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.26 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472669 n.824_825insTAGG non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472678 n.833_834delTTinsGCC non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472684 n.839_845delGGGATCCinsA non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.45 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.46 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.47 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.46 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.47 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475015 n.1358C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.73 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.74 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.72 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.57 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834222 c.681T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834225 c.684C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834261 c.720A>C synonymous_variant 0.19 pyrazinamide
rpsA 1834264 c.723G>C synonymous_variant 0.2 pyrazinamide
rpsA 1834297 c.756C>G synonymous_variant 0.18 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.17 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>A synonymous_variant 0.14 pyrazinamide
rpsA 1834396 c.855G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.15 pyrazinamide
tsnR 1853872 c.267G>T synonymous_variant 1.0 linezolid
tlyA 1917989 p.Ala17Gly missense_variant 0.98 capreomycin
bacA 2063805 c.924G>A synonymous_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
bacA 2064585 c.144C>A synonymous_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
ndh 2102525 p.Phe173Tyr missense_variant 0.98 isoniazid
delamanid
ethionamide
ndh 2102538 c.504_505insT frameshift_variant 0.98 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
Rv1979c 2222978 p.Ile63Phe missense_variant 1.0 bedaquiline
clofazimine
Rv1979c 2223052 p.Glu38Val missense_variant 1.0 bedaquiline
clofazimine
pncA 2289415 c.-174C>G upstream_gene_variant 1.0 pyrazinamide
kasA 2518057 c.-58A>C upstream_gene_variant 1.0 isoniazid
kasA 2518799 p.Pro229Ser missense_variant 0.94 isoniazid
eis 2714983 p.Ala117Glu missense_variant 1.0 kanamycin
amikacin
Rv2477c 2783502 c.541T>C synonymous_variant 0.14 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783512 c.531A>G synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783520 c.523T>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin
Rv2477c 2783548 c.495T>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783551 c.492G>A synonymous_variant 0.14 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783563 c.480A>G synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783569 c.474C>G synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783572 c.471A>G synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783578 p.Glu155Asp missense_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783586 p.Ala153Pro missense_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783593 c.450T>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783596 c.447C>T synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783605 c.438T>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783611 c.432C>G synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783628 p.Ala139Ser missense_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783629 c.414C>T synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783641 c.402G>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2784409 c.-367T>A upstream_gene_variant 0.88 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2784611 c.-569A>T upstream_gene_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyX 3067304 c.642A>G synonymous_variant 0.15 para-aminosalicylic_acid
thyX 3067316 c.630A>G synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067325 c.621A>G synonymous_variant 0.15 para-aminosalicylic_acid
thyX 3067355 c.591A>C synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067367 c.579G>C synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067376 c.570G>C synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067391 c.555G>C synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067394 c.552G>C synonymous_variant 0.15 para-aminosalicylic_acid
thyX 3067412 c.534C>G synonymous_variant 0.18 para-aminosalicylic_acid
thyX 3067439 c.507A>G synonymous_variant 0.19 para-aminosalicylic_acid
thyX 3067445 c.501C>G synonymous_variant 0.18 para-aminosalicylic_acid
thyX 3067451 c.495G>A synonymous_variant 0.18 para-aminosalicylic_acid
thyX 3067457 c.489C>G synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067463 p.Ile161Val missense_variant 0.16 para-aminosalicylic_acid
thyX 3067466 c.480G>C synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067470 p.Asn159Ser missense_variant 0.15 para-aminosalicylic_acid
thyX 3067493 c.453A>G synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067500 p.Lys149Arg missense_variant 0.17 para-aminosalicylic_acid
thyX 3067515 p.Ser144Thr missense_variant 0.14 para-aminosalicylic_acid
lpqB 3624701 c.210T>C synonymous_variant 0.16 rifampicin
bedaquiline
lpqB 3624713 c.198C>T synonymous_variant 0.18 rifampicin
bedaquiline
lpqB 3624722 c.189C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
lpqB 3624725 c.186G>C synonymous_variant 0.18 rifampicin
bedaquiline
lpqB 3624728 c.183C>T synonymous_variant 0.18 rifampicin
bedaquiline
lpqB 3624749 c.162G>A synonymous_variant 0.19 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3624755 c.154_156delTTAinsCTG synonymous_variant 0.18 rifampicin
bedaquiline
lpqB 3624760 c.151C>T synonymous_variant 0.17 rifampicin
bedaquiline
lpqB 3624770 c.141T>C synonymous_variant 0.15 rifampicin
bedaquiline
mtrA 3627227 c.123T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
bedaquiline
fbiA 3640404 c.-139C>A upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
fbiB 3642056 c.522C>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
rpoA 3877967 p.Thr181Ser missense_variant 0.92 rifampicin Uncertain significance
rpoA 3877972 c.535delG frameshift_variant 0.93 rifampicin
rpoA 3878061 c.447G>C synonymous_variant 0.16 rifampicin
rpoA 3878067 c.441C>G synonymous_variant 0.16 rifampicin
rpoA 3878070 c.438T>C synonymous_variant 0.16 rifampicin
rpoA 3878894 c.-387A>G upstream_gene_variant 0.14 rifampicin
clpC1 4038748 p.Arg653Cys missense_variant 0.14 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039524 p.Phe394Tyr missense_variant 0.15 pyrazinamide
clpC1 4039547 c.1158C>G synonymous_variant 0.17 pyrazinamide
clpC1 4039553 c.1152C>G synonymous_variant 0.17 pyrazinamide
clpC1 4039562 c.1143C>G synonymous_variant 0.17 pyrazinamide
clpC1 4039565 c.1140G>C synonymous_variant 0.17 pyrazinamide
clpC1 4039576 p.Ala377Ser missense_variant 0.14 pyrazinamide
clpC1 4039586 c.1119G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039610 c.1095G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039622 c.1083C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.18 pyrazinamide
clpC1 4039777 c.927_928insG frameshift_variant 1.0 pyrazinamide
clpC1 4039789 p.Ser306Thr missense_variant 0.13 pyrazinamide
glpK 4138934 c.822A>C synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embB 4247545 p.Ser344Arg missense_variant 0.94 ethambutol Uncertain significance
aftB 4268812 p.Ser9Pro missense_variant 1.0 ethambutol