TB-Profiler result

Run: SRR1049673
Summary

Run ID: SRR1049673

Sample name:

Date: 2024-03-26T16:39:22.234922

Number of reads: 1415029

Percentage reads mapped: 22.37

Median coverage: 29.0

Strain: lineage3

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser441Ala Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid
ethambutol
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
rrs n.799C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ser91Pro Assoc w R
p.Asp94Asn Assoc w R
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
gyrA 7572 p.Ser91Pro missense_variant 0.36 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
gyrA 7581 p.Asp94Asn missense_variant 0.39 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761127 p.Ser441Ala missense_variant 0.23 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpsL 781822 p.Lys88Arg missense_variant 0.42 streptomycin Assoc w R
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance Mutation from literature
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.43 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 0.36 kanamycin Assoc w R
amikacin Assoc w R
capreomycin 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 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.98 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.95 rifampicin Not assoc w R
rpoB 761051 c.1245G>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761084 c.1278C>A synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761088 c.1282_1284delAGCinsTCG synonymous_variant 0.26 rifampicin
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.25 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.24 rifampicin
rpoB 761111 c.1305C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761126 c.1320G>C synonymous_variant 0.23 rifampicin
rpoB 761132 c.1326G>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761234 c.1428G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>C synonymous_variant 0.19 rifampicin
rpoB 761261 c.1455G>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761264 c.1458C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761276 c.1470G>C synonymous_variant 0.18 rifampicin
rpoB 761282 c.1476C>T synonymous_variant 0.19 rifampicin
rpoB 761961 p.Pro719Ser missense_variant 0.27 rifampicin Uncertain significance
rpoB 761973 p.His723Tyr missense_variant 0.36 rifampicin
rpoB 761980 p.Tyr725Phe missense_variant 0.42 rifampicin
rpoB 761987 c.2181C>T synonymous_variant 0.49 rifampicin
rpoB 761999 c.2193G>C synonymous_variant 0.47 rifampicin
rpoB 762002 c.2196C>G synonymous_variant 0.47 rifampicin
rpoB 762003 c.2197_2199delAACinsCG frameshift_variant&missense_variant 0.48 rifampicin
rpoB 762015 c.2209_2211delGAAinsCG frameshift_variant&missense_variant 0.49 rifampicin
rpoB 762020 p.Glu738Asp missense_variant 0.47 rifampicin
rpoB 762026 c.2220G>C synonymous_variant 0.48 rifampicin
rpoB 762030 p.Thr742Ser missense_variant 0.48 rifampicin
rpoB 762053 c.2247T>C synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoB 762057 p.Ile751Val missense_variant 0.4 rifampicin Uncertain significance
rpoB 762062 c.2256T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 762080 c.2274G>C synonymous_variant 0.22 rifampicin
rpoB 762185 c.2379G>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 762194 c.2388G>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoB 762245 c.2439G>T synonymous_variant 0.52 rifampicin
rpoB 762251 c.2445G>C synonymous_variant 0.52 rifampicin
rpoB 762254 c.2448T>G synonymous_variant 0.52 rifampicin
rpoB 762257 c.2451C>G synonymous_variant 0.53 rifampicin
rpoB 762273 p.Ala823Ser missense_variant 0.52 rifampicin
rpoB 762278 c.2472C>T synonymous_variant 0.42 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 762293 c.2487T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 762878 p.Ile1024Met missense_variant 0.28 rifampicin
rpoB 762879 c.3073_3075delATGinsCC frameshift_variant&missense_variant 0.27 rifampicin
rpoB 762887 c.3081G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 762896 c.-474G>C upstream_gene_variant 0.46 rifampicin
rpoB 762899 c.3093G>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoB 762917 c.3111C>G synonymous_variant 0.49 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 762980 c.-390T>C upstream_gene_variant 0.51 rifampicin
rpoC 762983 c.-387C>T upstream_gene_variant 0.49 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.48 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoB 763002 c.3197dupA frameshift_variant 0.39 rifampicin
rpoB 763006 c.3201delC frameshift_variant 0.38 rifampicin
rpoB 763014 c.3208_3210delATGinsCC frameshift_variant&missense_variant 0.42 rifampicin
rpoB 763017 p.Gln1071Glu missense_variant 0.42 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.57 rifampicin Not assoc w R
rpoB 763031 c.3225T>G synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoB 763034 c.3228C>G synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 763053 c.3247T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 763094 c.3288G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 763100 c.-270G>A upstream_gene_variant 0.38 rifampicin
rpoC 763103 c.-267G>C upstream_gene_variant 0.39 rifampicin
rpoB 763122 c.3316_3318delATCinsCG frameshift_variant&missense_variant 0.43 rifampicin
rpoB 763127 c.3321G>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 763130 p.Glu1108Asp missense_variant 0.39 rifampicin
rpoC 763136 c.-234C>A upstream_gene_variant 0.36 rifampicin
rpoC 763157 c.-213G>C upstream_gene_variant 0.32 rifampicin
rpoC 763160 c.-210G>C upstream_gene_variant 0.3 rifampicin
rpoB 763161 p.Leu1119Ile missense_variant 0.29 rifampicin
rpoB 763166 c.3360A>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763169 c.-201A>G upstream_gene_variant 0.29 rifampicin
rpoB 763170 p.Leu1122Met missense_variant 0.29 rifampicin
rpoC 763468 c.99G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763483 c.114G>C synonymous_variant 0.34 rifampicin
rpoC 763486 c.117T>G synonymous_variant 0.39 rifampicin
rpoC 763504 c.135C>A synonymous_variant 0.58 rifampicin
rpoC 763507 c.138G>C synonymous_variant 0.62 rifampicin
rpoC 763528 c.159G>C synonymous_variant 0.64 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.63 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.63 rifampicin
rpoC 763537 c.168C>T synonymous_variant 0.65 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.65 rifampicin Not assoc w R - Interim
rpoC 763550 p.Tyr61Ala missense_variant 0.65 rifampicin
rpoC 763570 c.201G>C synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoC 763585 c.216C>G synonymous_variant 0.72 rifampicin
rpoC 763621 c.252C>T synonymous_variant 0.72 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.68 rifampicin Not assoc w R - Interim
rpoC 763642 c.273G>C synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>C synonymous_variant 0.66 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>T synonymous_variant 0.65 rifampicin
rpoC 763696 c.327T>C synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoC 763699 c.330G>T synonymous_variant 0.57 rifampicin
rpoC 763708 c.339G>C synonymous_variant 0.49 rifampicin
rpoC 763709 c.340C>T synonymous_variant 0.48 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.47 rifampicin
rpoC 763726 c.357C>T synonymous_variant 0.49 rifampicin
rpoC 763729 c.360G>C synonymous_variant 0.51 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.52 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.5 rifampicin
rpoC 763751 p.Ile128Val missense_variant 0.46 rifampicin
rpoC 764461 c.1092A>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764491 c.1122G>C synonymous_variant 0.54 rifampicin
rpoC 764498 p.Ser377Ala missense_variant 0.52 rifampicin
rpoC 764503 c.1134G>C synonymous_variant 0.54 rifampicin
rpoC 764507 p.Ala380Ser missense_variant 0.55 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoC 764524 c.1155C>T synonymous_variant 0.59 rifampicin
rpoC 764527 c.1158C>T synonymous_variant 0.59 rifampicin Not assoc w R - Interim
rpoC 764533 c.1164C>T synonymous_variant 0.64 rifampicin
rpoC 764536 c.1167G>T synonymous_variant 0.66 rifampicin Not assoc w R - Interim
rpoC 764542 c.1173C>G synonymous_variant 0.7 rifampicin
rpoC 764548 c.1179G>A synonymous_variant 0.73 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.73 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.68 rifampicin Not assoc w R - Interim
rpoC 764578 c.1209C>G synonymous_variant 0.67 rifampicin
rpoC 764581 c.1212T>C synonymous_variant 0.67 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.68 rifampicin
rpoC 764611 c.1242G>C synonymous_variant 0.68 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.61 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoC 764662 c.1293G>C synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 764668 c.1299C>T synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 764701 c.1332C>G synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764705 p.Leu446Thr missense_variant 0.43 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 764737 c.1368G>C synonymous_variant 0.61 rifampicin
rpoC 764746 c.1377G>C synonymous_variant 0.61 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.59 rifampicin Not assoc w R - Interim
rpoC 764755 c.1386C>T synonymous_variant 0.59 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 764780 c.1411_1413delAGCinsTCG synonymous_variant 0.62 rifampicin
rpoC 764797 c.1428G>C synonymous_variant 0.65 rifampicin
rpoC 764803 c.1434C>T synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoC 764808 p.Arg480His missense_variant 0.59 rifampicin
rpoC 764812 c.1443C>G synonymous_variant 0.55 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 764843 p.Ala492Thr missense_variant 0.44 rifampicin
rpoC 764848 c.1479G>A synonymous_variant 0.45 rifampicin
rpoC 764858 c.1489_1491delTTGinsCC frameshift_variant&missense_variant 0.37 rifampicin
rpoC 764863 c.1494G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>G synonymous_variant 0.31 rifampicin
rpoC 764935 c.1566T>C synonymous_variant 0.16 rifampicin
rpoC 764948 c.1579_1581delTTGinsCC frameshift_variant&missense_variant 0.16 rifampicin
rpoC 764956 c.1587T>C synonymous_variant 0.17 rifampicin
rpoC 764957 p.Glu530Ser missense_variant 0.17 rifampicin
rpoC 764968 c.1599T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764998 c.1629G>C synonymous_variant 0.25 rifampicin
rpoC 765007 c.1638T>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 765008 c.1639T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 765014 p.Ala549Pro missense_variant 0.29 rifampicin
rpoC 765019 c.1650A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 765958 c.2589C>G synonymous_variant 0.29 rifampicin
rpoC 765962 c.2593T>C synonymous_variant 0.29 rifampicin
rpoC 765967 c.2598C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 765973 c.2604C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 765994 c.2625A>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 765997 c.2628T>C synonymous_variant 0.21 rifampicin
rpoC 766000 c.2631G>C synonymous_variant 0.23 rifampicin
rpoC 766003 c.2634G>C synonymous_variant 0.23 rifampicin
rpoC 766012 c.2643C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
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 1.0 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
rpsL 781760 c.201T>C synonymous_variant 0.32 streptomycin
rpsL 781766 c.207C>T synonymous_variant 0.38 streptomycin Not assoc w R - Interim
rpsL 781772 c.213C>A synonymous_variant 0.41 streptomycin
rpsL 781796 p.Met79Ile missense_variant 0.4 streptomycin
rpsL 781802 c.243G>C synonymous_variant 0.41 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.4 streptomycin
rpsL 781817 c.258G>T synonymous_variant 0.41 streptomycin
rpsL 781820 c.261G>C synonymous_variant 0.42 streptomycin
rpsL 781829 c.270G>T synonymous_variant 0.43 streptomycin
rpsL 781832 c.273T>G synonymous_variant 0.43 streptomycin
rpsL 781845 p.Lys96Arg missense_variant 0.35 streptomycin
rpsL 781851 c.292_294delATCinsGG frameshift_variant&missense_variant 0.38 streptomycin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472120 n.275G>A non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472245 n.400C>A non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472506 n.661A>T non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472572 n.727T>A non_coding_transcript_exon_variant 0.33 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.31 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472734 n.889C>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 1472952 n.1107T>C non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.4 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.45 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473047 n.1202C>T non_coding_transcript_exon_variant 0.42 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473122 n.1278A>T non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473157 n.1312C>T non_coding_transcript_exon_variant 0.42 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473288 n.1443delCinsAGTTT non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473298 n.1453A>G non_coding_transcript_exon_variant 0.34 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.36 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474806 n.1149A>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474822 n.1165G>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474905 n.1248T>A non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.37 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1476519 n.2862C>T non_coding_transcript_exon_variant 0.33 capreomycin
linezolid Uncertain significance
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476534 n.2877A>T non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673816 c.-386G>A upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1833668 p.Ile43Val missense_variant 0.41 pyrazinamide
rpsA 1833676 c.135A>G synonymous_variant 0.46 pyrazinamide
rpsA 1833679 c.138G>C synonymous_variant 0.46 pyrazinamide
rpsA 1833682 c.141C>T synonymous_variant 0.45 pyrazinamide
rpsA 1833685 c.144G>C synonymous_variant 0.45 pyrazinamide
rpsA 1833694 c.153G>C synonymous_variant 0.41 pyrazinamide
rpsA 1833698 p.Leu53Val missense_variant 0.36 pyrazinamide
rpsA 1833709 c.168C>A synonymous_variant 0.36 pyrazinamide
rpsA 1833718 c.177C>G synonymous_variant 0.29 pyrazinamide
rpsA 1834039 c.498C>G synonymous_variant 0.26 pyrazinamide
rpsA 1834040 p.Lys167Gln missense_variant 0.26 pyrazinamide
rpsA 1834043 p.Glu168Gln missense_variant 0.26 pyrazinamide
rpsA 1834046 p.Ile169Val missense_variant 0.29 pyrazinamide
rpsA 1834054 c.513C>G synonymous_variant 0.26 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834090 c.549G>C synonymous_variant 0.26 pyrazinamide
rpsA 1834093 c.552G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834096 c.555G>C synonymous_variant 0.23 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.23 pyrazinamide
rpsA 1834102 c.561T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834114 c.573G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834210 c.669C>T synonymous_variant 0.27 pyrazinamide
rpsA 1834213 c.672G>C synonymous_variant 0.27 pyrazinamide
rpsA 1834222 c.681T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834228 c.687C>T synonymous_variant 0.23 pyrazinamide
rpsA 1834234 c.693G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834240 c.699T>A synonymous_variant 0.24 pyrazinamide
rpsA 1834243 c.702G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834255 c.714C>G synonymous_variant 0.23 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834279 c.738C>T synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
rpsA 1834327 c.786G>T synonymous_variant 0.41 pyrazinamide
rpsA 1834348 c.807T>G synonymous_variant 0.41 pyrazinamide
rpsA 1834354 c.813G>C synonymous_variant 0.41 pyrazinamide Not assoc w R - Interim
rpsA 1834357 c.816T>C synonymous_variant 0.4 pyrazinamide
rpsA 1834361 c.820_822delTTGinsCC frameshift_variant&missense_variant 0.41 pyrazinamide Uncertain significance
rpsA 1834366 c.825A>G synonymous_variant 0.49 pyrazinamide Not assoc w R - Interim
rpsA 1834378 c.837T>G synonymous_variant 0.64 pyrazinamide
rpsA 1834387 c.846C>T synonymous_variant 0.66 pyrazinamide
rpsA 1834395 p.Arg285Gln missense_variant 0.68 pyrazinamide
rpsA 1834408 c.867C>G synonymous_variant 0.67 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.65 pyrazinamide
rpsA 1834416 p.Ala292Val missense_variant 0.66 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.71 pyrazinamide
rpsA 1834451 c.910_912delTTGinsCC frameshift_variant&missense_variant 0.74 pyrazinamide Uncertain significance
rpsA 1834468 c.927A>G synonymous_variant 0.7 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.66 pyrazinamide
rpsA 1834486 p.Glu315Asp missense_variant 0.58 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.57 pyrazinamide
rpsA 1834501 c.960G>C synonymous_variant 0.43 pyrazinamide
rpsA 1834504 c.963G>C synonymous_variant 0.42 pyrazinamide
rpsA 1834519 c.978G>C synonymous_variant 0.32 pyrazinamide
rpsA 1834524 p.Glu328Val missense_variant 0.28 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.24 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 0.95 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser 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
pncA 2289047 c.195C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 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
thyX 3067987 c.-42C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
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
rpoA 3877803 c.705G>C synonymous_variant 0.2 rifampicin
rpoA 3877824 c.684G>A synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoA 3877836 c.672A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>T synonymous_variant 0.21 rifampicin
rpoA 3877842 c.666A>C synonymous_variant 0.21 rifampicin
rpoA 3877845 c.663G>C synonymous_variant 0.21 rifampicin
rpoA 3877848 c.660C>A synonymous_variant 0.22 rifampicin
rpoA 3877856 c.652T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoA 3877866 c.642G>C synonymous_variant 0.23 rifampicin
rpoA 3877875 c.633T>G synonymous_variant 0.23 rifampicin
rpoA 3877878 c.630G>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
clpC1 4039976 p.Lys243Thr missense_variant 0.4 pyrazinamide
clpC1 4039982 p.Thr241Ile missense_variant 0.4 pyrazinamide
clpC1 4039991 c.714G>T synonymous_variant 0.52 pyrazinamide
clpC1 4040002 p.His235Asn missense_variant 0.54 pyrazinamide
clpC1 4040003 c.702G>C synonymous_variant 0.54 pyrazinamide
clpC1 4040009 c.696C>G synonymous_variant 0.57 pyrazinamide
clpC1 4040021 c.684A>T synonymous_variant 0.57 pyrazinamide
clpC1 4040024 c.681A>G synonymous_variant 0.56 pyrazinamide
clpC1 4040030 c.675C>G synonymous_variant 0.55 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.57 pyrazinamide
clpC1 4040063 c.642G>C synonymous_variant 0.53 pyrazinamide Not assoc w R - Interim
clpC1 4040066 c.639G>T synonymous_variant 0.52 pyrazinamide
clpC1 4040081 c.624C>G synonymous_variant 0.43 pyrazinamide
clpC1 4040087 c.618G>C synonymous_variant 0.31 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.96 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 4242075 p.Arg738Gln missense_variant 0.94 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247358 p.Val282Ala missense_variant 0.74 ethambutol Uncertain significance
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 1.0 streptomycin Not assoc w R