TB-Profiler result

Run: ERR978726
Summary

Run ID: ERR978726

Sample name:

Date: 2024-03-25T18:55:13.237540

Number of reads: 1441754

Percentage reads mapped: 33.11

Median coverage: 44.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: RR-TB

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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
lineage4.8 Euro-American (mainly T) RD219 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB c.1321_1323delTCGinsGC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Gly442Glu Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Leu443Met Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
rpoB 761127 c.1321_1323delTCGinsGC frameshift_variant&missense_variant 0.19 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761131 p.Gly442Glu missense_variant 0.19 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761133 p.Leu443Met missense_variant 0.2 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.84 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 0.74 capreomycin Assoc w R
kanamycin Assoc w R
amikacin 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
Rv0565c 656265 c.1204_1205delAC frameshift_variant 1.0 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 761063 c.1257C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761084 c.1278C>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.14 rifampicin
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.15 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.15 rifampicin
rpoB 761111 c.1305C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761147 c.1341C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 762879 p.Met1025Leu missense_variant 0.15 rifampicin Uncertain significance
rpoC 762899 c.-471G>T upstream_gene_variant 0.2 rifampicin
rpoB 762920 c.3114C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 762959 c.-411G>T upstream_gene_variant 0.19 rifampicin
rpoC 762971 c.-399G>C upstream_gene_variant 0.16 rifampicin
rpoC 762983 c.-387C>T upstream_gene_variant 0.16 rifampicin
rpoB 762989 c.3183G>A synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762995 c.3189G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763002 c.3197dupA frameshift_variant 0.18 rifampicin
rpoB 763006 c.3201delC frameshift_variant 0.18 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763534 c.165T>C synonymous_variant 0.23 rifampicin
rpoC 763537 c.168C>G synonymous_variant 0.23 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763622 p.Ala85Ser missense_variant 0.16 rifampicin Uncertain significance
rpoC 763627 p.Lys86Asn missense_variant 0.14 rifampicin Uncertain significance
rpoC 763642 c.273G>T synonymous_variant 0.17 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781275 c.-285A>C upstream_gene_variant 1.0 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472085 n.240C>T non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472107 n.262A>G non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.64 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 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.65 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.61 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.56 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.43 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472288 n.443A>T non_coding_transcript_exon_variant 0.2 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472290 n.445C>T non_coding_transcript_exon_variant 0.2 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472298 n.453_467delGTCCGGGTTCTCTCGinsCGT non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472324 n.479G>A non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472325 n.480G>T non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472326 n.481T>G non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472329 n.484A>T non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472330 n.485G>A non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.28 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 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.47 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.72 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.78 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.8 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.81 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.81 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.81 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.82 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.87 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.92 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.86 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.74 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.64 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 0.83 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.83 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.83 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.85 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.84 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.85 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.83 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473094 n.1249T>G non_coding_transcript_exon_variant 0.44 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473100 n.1255G>C non_coding_transcript_exon_variant 0.44 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.43 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473120 n.1275C>T non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.43 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 0.44 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.61 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.61 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.75 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.83 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.82 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.78 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.77 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.78 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.77 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.75 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid
rrl 1474202 n.545T>G non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1474218 n.561T>G non_coding_transcript_exon_variant 0.61 capreomycin
linezolid
rrl 1474253 n.596A>T non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474264 n.607T>G non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1474265 n.608G>T non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474269 n.612C>A non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1474271 n.614A>G non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1474287 n.631_649delCCTTTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 0.64 capreomycin
linezolid
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474444 n.787G>C non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474467 n.810A>T non_coding_transcript_exon_variant 0.66 capreomycin
linezolid
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.75 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.76 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.75 capreomycin
linezolid
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.75 capreomycin
linezolid
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.75 capreomycin
linezolid
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.76 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid
rrl 1475756 n.2099_2107delTAACCCGCAinsG non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.76 capreomycin
linezolid Uncertain significance
rrl 1475770 n.2113_2114delGAinsATGCGT non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.67 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475991 n.2334T>A non_coding_transcript_exon_variant 0.66 capreomycin
linezolid
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.66 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475996 n.2339T>G non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.62 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.62 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.61 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.61 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.61 capreomycin
linezolid
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476288 n.2635_2643delGCACCCCCG non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476301 n.2644_2645insCGGTGGCTT non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476316 n.2659G>A non_coding_transcript_exon_variant 0.67 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.85 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.69 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rpsA 1833952 c.411C>A synonymous_variant 0.33 pyrazinamide
rpsA 1833955 c.414G>T synonymous_variant 0.34 pyrazinamide
rpsA 1833958 c.417C>T synonymous_variant 0.35 pyrazinamide
rpsA 1833959 p.Leu140Val missense_variant 0.36 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.49 pyrazinamide
rpsA 1833976 c.435C>T synonymous_variant 0.48 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.52 pyrazinamide
rpsA 1833985 c.444G>T synonymous_variant 0.53 pyrazinamide
rpsA 1833994 c.453G>C synonymous_variant 0.54 pyrazinamide
rpsA 1833997 c.456G>T synonymous_variant 0.54 pyrazinamide
rpsA 1834000 c.459G>T synonymous_variant 0.54 pyrazinamide
rpsA 1834012 c.471G>A synonymous_variant 0.54 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.57 pyrazinamide
rpsA 1834018 c.477C>T synonymous_variant 0.56 pyrazinamide
rpsA 1834024 c.483G>C synonymous_variant 0.56 pyrazinamide
rpsA 1834034 c.493_495delATCinsGG frameshift_variant&missense_variant 0.54 pyrazinamide Uncertain significance
rpsA 1834039 c.498C>T synonymous_variant 0.54 pyrazinamide
rpsA 1834040 p.Lys167Gln missense_variant 0.54 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.52 pyrazinamide
rpsA 1834090 c.549G>T synonymous_variant 0.39 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.37 pyrazinamide
rpsA 1834105 c.564C>T synonymous_variant 0.36 pyrazinamide
rpsA 1834108 c.567C>G synonymous_variant 0.35 pyrazinamide
rpsA 1834114 c.573G>C synonymous_variant 0.25 pyrazinamide
rpsA 1834123 c.582C>T synonymous_variant 0.21 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834273 c.732C>T synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
rpsA 1834287 p.Ser249Cys missense_variant 0.13 pyrazinamide
rpsA 1834298 p.Gln253Glu missense_variant 0.14 pyrazinamide
rpsA 1834307 c.766_768delGACinsCG frameshift_variant&missense_variant 0.15 pyrazinamide Uncertain significance
rpsA 1834310 p.Glu257Pro missense_variant 0.15 pyrazinamide
rpsA 1834318 c.777C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834330 c.789C>G synonymous_variant 0.15 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918631 p.Pro231Arg missense_variant 1.0 capreomycin
PPE35 2168149 p.Pro822Ser missense_variant 1.0 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv3083 3448499 c.-4_*1408del transcript_ablation 1.0 ethionamide Uncertain significance
Rv3236c 3613636 c.-520A>G upstream_gene_variant 1.0 pyrazinamide Not assoc w R
mtrA 3627020 c.330G>A synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
clpC1 4039729 p.Asp326Asn missense_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R