TB-Profiler result

Run: ERR2514430
Summary

Run ID: ERR2514430

Sample name:

Date: 2024-03-25T22:56:24.216891

Number of reads: 3407055

Percentage reads mapped: 87.48

Median coverage: 114.0

Strain: lineage3.1.2;lineage4.1.1.3.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.23
lineage3.1.2 East-African-Indian RD750 0.24
lineage4.1 Euro-American None 0.75
lineage4.1.1.3 Euro-American (X-type) RD193 0.72
lineage4 Euro-American None 0.76
lineage4.1.1 Euro-American (X-type) None 0.77
lineage4.1.1.3.1 Euro-American (X-type) RD193 0.75
lineage3.1 East-African-Indian RD750 0.39
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 rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
n.1484G>T Assoc w R
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance Mutation from literature
amikacin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.47 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.26 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.25 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.83 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.21 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.24 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.26 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.72 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.26 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.72 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.28 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303601 p.Glu224Gly missense_variant 0.73 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471972 n.127T>C non_coding_transcript_exon_variant 0.1 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471981 n.136C>G non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472009 n.164T>G non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472085 n.240C>T non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472107 n.262A>G non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.54 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.53 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.49 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.39 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472288 n.443A>T non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472290 n.445C>T non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472298 n.453_467delGTCCGGGTTCTCTCGinsCGT non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472324 n.479G>A non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472325 n.480G>T non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472326 n.481T>G non_coding_transcript_exon_variant 0.31 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472329 n.484A>T non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472330 n.485G>A non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.51 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.51 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.65 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.7 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.69 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.67 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.68 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.7 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.7 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.61 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.49 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472812 n.967A>T non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.6 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.6 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.59 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.58 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.57 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.61 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473094 n.1249T>G non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>C non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473120 n.1275C>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473122 n.1277T>G non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.54 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.6 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.51 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.51 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.52 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.48 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474265 n.608G>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474269 n.612C>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474287 n.631_649delCCTTTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474467 n.810A>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.49 capreomycin
linezolid
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.49 capreomycin
linezolid
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid
rrl 1475756 n.2099_2107delTAACCCGCAinsG non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.49 capreomycin
linezolid Uncertain significance
rrl 1475770 n.2113_2114delGAinsATGCGT non_coding_transcript_exon_variant 0.49 capreomycin
linezolid
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.26 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476316 n.2659G>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.49 capreomycin
linezolid
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.5 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833959 p.Leu140Val missense_variant 0.1 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833976 c.435C>T synonymous_variant 0.15 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.16 pyrazinamide
rpsA 1833985 c.444G>T synonymous_variant 0.17 pyrazinamide
rpsA 1833994 c.453G>T synonymous_variant 0.18 pyrazinamide
rpsA 1833997 c.456G>T synonymous_variant 0.19 pyrazinamide
rpsA 1834000 c.459G>T synonymous_variant 0.18 pyrazinamide
rpsA 1834012 c.471G>A synonymous_variant 0.18 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834018 c.477C>T synonymous_variant 0.18 pyrazinamide
rpsA 1834024 c.483G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834034 c.493_495delATCinsGG frameshift_variant&missense_variant 0.17 pyrazinamide Uncertain significance
rpsA 1834039 c.498C>T synonymous_variant 0.18 pyrazinamide
rpsA 1834040 p.Lys167Gln missense_variant 0.17 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.19 pyrazinamide
rpsA 1834090 c.549G>T synonymous_variant 0.11 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.1 pyrazinamide
rpsA 1834108 c.567C>G synonymous_variant 0.1 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 0.2 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.27 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.24 pyrazinamide 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
Rv1979c 2223372 c.-208C>G upstream_gene_variant 0.81 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.23 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.3 pyrazinamide
kasA 2518245 p.His44Arg missense_variant 0.16 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.27 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.19 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
ddn 3986804 c.-40C>T upstream_gene_variant 0.23 delamanid
pretomanid
panD 4044872 c.-591C>T upstream_gene_variant 0.32 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.19 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4239235 c.-628C>T upstream_gene_variant 0.24 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.29 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.75 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.72 ethambutol Not assoc w R
ubiA 4269540 c.294C>T synonymous_variant 0.75 ethambutol Not assoc w R
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 4407588 c.615A>G synonymous_variant 0.24 streptomycin Not assoc w R