TB-Profiler result

Run: ERR2514552
Summary

Run ID: ERR2514552

Sample name:

Date: 2024-04-14T23:32:48.397277

Number of reads: 664645

Percentage reads mapped: 57.77

Median coverage: 20.0

Strain: lineage3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 1.0
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
capreomycin
kanamycin
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
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
dnaA 693 c.693A>C synonymous_variant 0.22 isoniazid
dnaA 705 c.705A>G synonymous_variant 0.22 isoniazid
dnaA 708 c.708T>C synonymous_variant 0.25 isoniazid
dnaA 720 c.720G>A synonymous_variant 0.34 isoniazid
dnaA 741 c.741T>C synonymous_variant 0.35 isoniazid Not assoc w R - Interim
dnaA 747 c.747G>T synonymous_variant 0.36 isoniazid
dnaA 748 c.748_750delCTCinsTG frameshift_variant&missense_variant 0.4 isoniazid Uncertain significance
dnaA 763 p.Lys255Arg missense_variant 0.38 isoniazid
dnaA 771 c.771A>G synonymous_variant 0.4 isoniazid
dnaA 793 c.793_795delGTAinsAC frameshift_variant&missense_variant 0.39 isoniazid Uncertain significance
dnaA 801 c.801G>T synonymous_variant 0.36 isoniazid
dnaA 804 c.804G>C synonymous_variant 0.36 isoniazid
dnaA 805 c.805_807delTTGinsCC frameshift_variant&missense_variant 0.38 isoniazid Uncertain significance
dnaA 822 c.822A>G synonymous_variant 0.38 isoniazid
dnaA 828 c.828T>C synonymous_variant 0.39 isoniazid Not assoc w R - Interim
dnaA 837 c.837A>G synonymous_variant 0.33 isoniazid
dnaA 840 c.840G>A synonymous_variant 0.32 isoniazid
dnaA 846 c.846T>C synonymous_variant 0.31 isoniazid
dnaA 849 c.849A>G synonymous_variant 0.31 isoniazid
dnaA 852 c.852G>A synonymous_variant 0.33 isoniazid Not assoc w R - Interim
gyrA 7066 c.-236G>T upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 7081 c.-221T>C upstream_gene_variant 0.24 levofloxacin
moxifloxacin
gyrA 7084 c.-218A>G upstream_gene_variant 0.28 levofloxacin
moxifloxacin
gyrA 7090 c.-212C>T upstream_gene_variant 0.31 levofloxacin
moxifloxacin
gyrB 7093 c.1854T>C synonymous_variant 0.3 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 7100 c.1861T>C synonymous_variant 0.39 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7123 c.-179C>G upstream_gene_variant 0.36 levofloxacin
moxifloxacin
gyrB 7126 c.1887G>C synonymous_variant 0.33 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7129 c.-173T>G upstream_gene_variant 0.32 levofloxacin
moxifloxacin
gyrA 7132 c.-170T>C upstream_gene_variant 0.33 levofloxacin
moxifloxacin
gyrA 7135 c.-167G>A upstream_gene_variant 0.33 levofloxacin
moxifloxacin
gyrA 7136 c.-166T>C upstream_gene_variant 0.35 levofloxacin
moxifloxacin
gyrA 7141 c.-161T>G upstream_gene_variant 0.37 levofloxacin
moxifloxacin
gyrA 7144 c.-158A>G upstream_gene_variant 0.37 levofloxacin
moxifloxacin
gyrA 7150 c.-152G>A upstream_gene_variant 0.39 levofloxacin
moxifloxacin
gyrB 7153 c.1914G>C synonymous_variant 0.38 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7168 c.-134C>G upstream_gene_variant 0.37 levofloxacin
moxifloxacin
gyrA 7178 c.-124T>C upstream_gene_variant 0.39 levofloxacin
moxifloxacin
gyrB 7186 c.1947C>G synonymous_variant 0.37 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7189 c.-113C>T upstream_gene_variant 0.32 levofloxacin
moxifloxacin
gyrB 7198 c.1959C>T synonymous_variant 0.3 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrB 7210 p.Asp657Glu missense_variant 0.24 levofloxacin
moxifloxacin
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 7607 c.306C>T synonymous_variant 0.25 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8870 c.1569G>C synonymous_variant 0.34 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8873 c.1572A>G synonymous_variant 0.34 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8897 c.1596T>C synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8903 c.1602T>C synonymous_variant 0.28 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8915 c.1614A>G synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8924 c.1623C>T synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 8942 c.1641G>C synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
hadA 732145 c.216C>T synonymous_variant 1.0 isoniazid Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 760522 p.Ser239Asn missense_variant 0.48 rifampicin Uncertain significance
rpoB 760532 c.726T>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoB 760541 c.735G>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoB 760553 c.747C>G synonymous_variant 0.52 rifampicin
rpoB 760561 c.757_758delCG frameshift_variant 0.37 rifampicin
rpoB 760567 p.Ser254Trp missense_variant 0.36 rifampicin
rpoB 760568 c.762_763insGC frameshift_variant 0.36 rifampicin
rpoB 760571 c.765G>C synonymous_variant 0.34 rifampicin
rpoB 760588 p.Thr261Ile missense_variant 0.36 rifampicin
rpoB 760591 p.Val262Ala missense_variant 0.36 rifampicin
rpoB 760595 c.789C>T synonymous_variant 0.36 rifampicin
rpoB 760596 p.Thr264Pro missense_variant 0.38 rifampicin
rpoB 760608 c.802C>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoB 760611 c.805T>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 760634 c.828T>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 760655 c.849A>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
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 761060 c.1254C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761063 c.1257C>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 761084 c.1278C>A synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.36 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.36 rifampicin
rpoB 761132 c.1326G>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761537 c.1731C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 761555 c.1749G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761558 c.1752C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 761564 c.1758G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 0.31 rifampicin
rpoB 761612 c.1806G>T synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.41 rifampicin
rpoB 761657 c.1851C>T synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 761669 c.1863C>T synonymous_variant 0.35 rifampicin
rpoB 761675 c.1869G>C synonymous_variant 0.27 rifampicin
rpoB 761705 c.1899C>A synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.41 rifampicin Uncertain significance
rpoB 762176 c.2370T>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 762194 c.2388G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.8 rifampicin Not assoc w R
rpoB 762894 c.3088C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 762899 c.3093G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762917 c.3111C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 762959 c.3153G>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.72 rifampicin Not assoc w R
rpoC 763468 c.99G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763492 c.123G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 763531 c.162G>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 763609 c.240C>T synonymous_variant 0.37 rifampicin
rpoC 763621 c.252C>T synonymous_variant 0.32 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764509 c.1140G>A synonymous_variant 0.32 rifampicin
rpoC 764510 c.1141C>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764530 c.1161C>T synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764533 c.1164C>A synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764545 c.1176C>A synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764593 c.1224C>T synonymous_variant 0.39 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764668 c.1299C>T synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764683 c.1314G>A synonymous_variant 0.45 rifampicin
rpoC 764692 c.1323C>T synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 764713 c.1344G>T synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.19 rifampicin Not assoc w R
rpoC 764810 p.Pro481Ala missense_variant 0.21 rifampicin Uncertain significance
rpoC 764815 c.1446A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764869 c.1500C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>A synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 764887 c.1518G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.2 rifampicin
rpoC 764912 p.Met515Gln missense_variant 0.2 rifampicin Uncertain significance
rpoC 764932 c.1563C>A synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 765383 p.Met672Leu missense_variant 0.32 rifampicin Uncertain significance
rpoC 765403 c.2034G>C synonymous_variant 0.44 rifampicin
rpoC 765405 p.Leu679His missense_variant 0.44 rifampicin Uncertain significance
rpoC 765409 c.2040T>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 765421 c.2052C>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 765449 c.2080_2082delGCCinsTG frameshift_variant&missense_variant 0.42 rifampicin
rpoC 765454 c.2085C>G synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 765469 c.2100G>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>G synonymous_variant 0.4 rifampicin
rpoC 765480 p.Tyr704Phe missense_variant 0.38 rifampicin Uncertain significance
rpoC 765499 c.2130C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 766570 c.3201T>C synonymous_variant 0.33 rifampicin
rpoC 766573 c.3204T>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 766594 c.3225G>T synonymous_variant 0.33 rifampicin
rpoC 766607 p.Ile1080Leu missense_variant 0.38 rifampicin
rpoC 766618 c.3249G>T synonymous_variant 0.31 rifampicin
rpoC 766624 c.3255G>C synonymous_variant 0.32 rifampicin
rpoC 766630 c.3261G>C synonymous_variant 0.32 rifampicin
rpoC 766633 c.3264G>C synonymous_variant 0.31 rifampicin
rpoC 766642 c.3273C>T synonymous_variant 0.3 rifampicin
rpoC 766645 c.3276A>G synonymous_variant 0.28 rifampicin
rpoC 766651 c.3282T>C synonymous_variant 0.23 rifampicin
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 781706 c.147T>C synonymous_variant 0.24 streptomycin
rpsL 781802 c.243G>C synonymous_variant 0.27 streptomycin
rpsL 781814 c.255C>T synonymous_variant 0.31 streptomycin
rpsL 781817 c.258G>T synonymous_variant 0.31 streptomycin
rpsL 781829 c.270G>C synonymous_variant 0.3 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.3 streptomycin
rpsL 781859 c.300T>C synonymous_variant 0.34 streptomycin Not assoc w R - Interim
rpsL 781868 c.309T>C synonymous_variant 0.34 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.31 streptomycin
rpsL 781877 c.318T>A synonymous_variant 0.28 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.3 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.3 streptomycin
rpsL 781907 c.348T>C synonymous_variant 0.31 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.31 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.26 streptomycin Uncertain significance
rpsL 781933 c.374G>A splice_region_variant&stop_retained_variant 0.27 streptomycin
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
sigE 1364703 c.291G>C synonymous_variant 0.19 pyrazinamide
sigE 1364709 c.297T>G synonymous_variant 0.18 pyrazinamide
sigE 1364712 c.300T>C synonymous_variant 0.18 pyrazinamide
sigE 1364718 c.306C>T synonymous_variant 0.2 pyrazinamide
sigE 1364726 p.Asn105Ser missense_variant 0.2 pyrazinamide
atpE 1461149 c.105T>G synonymous_variant 0.5 bedaquiline
atpE 1461161 c.117C>G synonymous_variant 0.47 bedaquiline
atpE 1461164 c.120C>T synonymous_variant 0.45 bedaquiline
atpE 1461167 c.123G>T synonymous_variant 0.45 bedaquiline
atpE 1461170 c.126A>G synonymous_variant 0.45 bedaquiline
atpE 1461179 c.135G>T synonymous_variant 0.45 bedaquiline
atpE 1461182 c.138A>G synonymous_variant 0.43 bedaquiline
atpE 1461185 c.141G>C synonymous_variant 0.41 bedaquiline
atpE 1461197 c.153A>C synonymous_variant 0.39 bedaquiline
atpE 1461219 c.175T>C synonymous_variant 0.39 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833619 c.78A>C synonymous_variant 0.33 pyrazinamide
rpsA 1833625 c.84A>G synonymous_variant 0.32 pyrazinamide
rpsA 1833664 c.123C>G synonymous_variant 0.37 pyrazinamide
rpsA 1833676 c.135A>G synonymous_variant 0.33 pyrazinamide
rpsA 1833679 c.138G>T synonymous_variant 0.33 pyrazinamide
rpsA 1833685 c.144G>C synonymous_variant 0.35 pyrazinamide
rpsA 1833691 c.150G>A synonymous_variant 0.31 pyrazinamide
rpsA 1833760 c.219C>T synonymous_variant 0.38 pyrazinamide Not assoc w R - Interim
rpsA 1833787 c.246C>G synonymous_variant 0.31 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.31 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.31 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.32 pyrazinamide
rpsA 1833823 c.282G>A synonymous_variant 0.33 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.34 pyrazinamide
rpsA 1833835 c.294C>T synonymous_variant 0.34 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.34 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.35 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.36 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.42 pyrazinamide
rpsA 1833874 c.333T>G synonymous_variant 0.41 pyrazinamide
rpsA 1833877 c.336C>G synonymous_variant 0.41 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.42 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.42 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.41 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.5 pyrazinamide
rpsA 1833958 c.417C>T synonymous_variant 0.47 pyrazinamide
rpsA 1833961 c.420C>G synonymous_variant 0.47 pyrazinamide
rpsA 1833970 c.429G>T synonymous_variant 0.5 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.55 pyrazinamide
rpsA 1833991 c.450C>G synonymous_variant 0.55 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.52 pyrazinamide
rpsA 1834009 c.468C>T synonymous_variant 0.46 pyrazinamide
rpsA 1834012 c.471G>C synonymous_variant 0.48 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.48 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.47 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.46 pyrazinamide
rpsA 1834073 p.Lys178Arg missense_variant 0.34 pyrazinamide
rpsA 1834096 c.555G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.23 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.24 pyrazinamide
rpsA 1834246 c.705G>T synonymous_variant 0.24 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.25 pyrazinamide
rpsA 1834252 c.711C>G synonymous_variant 0.26 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.32 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.32 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.32 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834438 c.897C>T synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
rpsA 1834451 c.910T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.38 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.44 pyrazinamide
rpsA 1834477 c.936C>T synonymous_variant 0.44 pyrazinamide Not assoc w R - Interim
rpsA 1834489 c.948T>C synonymous_variant 0.48 pyrazinamide
rpsA 1834516 c.975G>A synonymous_variant 0.52 pyrazinamide
rpsA 1834519 c.978G>C synonymous_variant 0.57 pyrazinamide
rpsA 1834520 c.979_981delGCCinsTG frameshift_variant&missense_variant 0.57 pyrazinamide Uncertain significance
rpsA 1834528 c.987T>C synonymous_variant 0.54 pyrazinamide
rpsA 1834543 c.1002C>G synonymous_variant 0.52 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.5 pyrazinamide
rpsA 1834552 c.1011G>T synonymous_variant 0.5 pyrazinamide
rpsA 1834555 c.1014T>G synonymous_variant 0.48 pyrazinamide
rpsA 1834557 p.Ala339Gly missense_variant 0.48 pyrazinamide
rpsA 1834606 c.1065C>T synonymous_variant 0.48 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.43 pyrazinamide
rpsA 1834619 c.1078T>C synonymous_variant 0.4 pyrazinamide
rpsA 1834622 c.1081_1083delTCGinsAGC synonymous_variant 0.42 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.42 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834645 c.1104C>T synonymous_variant 0.33 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 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
kasA 2517917 c.-198G>C upstream_gene_variant 0.63 isoniazid
kasA 2517941 c.-174C>G upstream_gene_variant 0.61 isoniazid
kasA 2517953 c.-162C>T upstream_gene_variant 0.6 isoniazid
kasA 2517962 c.-153C>G upstream_gene_variant 0.52 isoniazid
kasA 2517968 c.-147T>A upstream_gene_variant 0.55 isoniazid
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
Rv2477c 2783485 c.558G>C synonymous_variant 0.33 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783491 c.552C>T synonymous_variant 0.3 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783499 c.544T>C synonymous_variant 0.27 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783502 c.541T>C synonymous_variant 0.27 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783509 c.534C>A synonymous_variant 0.27 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783512 c.531A>G synonymous_variant 0.26 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783515 c.528C>G synonymous_variant 0.26 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783520 c.523T>C synonymous_variant 0.24 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin Not assoc w R - Interim
amikacin
Rv2477c 2783523 c.520C>T synonymous_variant 0.24 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783527 c.516A>G synonymous_variant 0.24 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783548 c.495T>C synonymous_variant 0.27 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3626717 c.-104C>T upstream_gene_variant 0.26 bedaquiline
rifampicin
mtrB 3626726 c.-113T>C upstream_gene_variant 0.29 bedaquiline
rifampicin
mtrB 3626732 c.-119A>G upstream_gene_variant 0.28 bedaquiline
rifampicin
mtrA 3626741 c.609C>G synonymous_variant 0.26 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626756 c.594C>G synonymous_variant 0.27 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626759 c.591T>C synonymous_variant 0.27 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626762 c.588G>C synonymous_variant 0.28 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626786 c.564A>G synonymous_variant 0.36 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626792 c.558G>T synonymous_variant 0.35 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626804 c.546A>G synonymous_variant 0.29 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626825 c.525T>A synonymous_variant 0.22 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627098 c.252A>C synonymous_variant 0.35 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627110 c.-497G>C upstream_gene_variant 0.35 bedaquiline
rifampicin
mtrA 3627119 c.231T>G synonymous_variant 0.32 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627122 c.-509T>G upstream_gene_variant 0.32 bedaquiline
rifampicin
mtrB 3627128 c.-515T>C upstream_gene_variant 0.3 bedaquiline
rifampicin
mtrA 3627133 p.Ala73Ser missense_variant 0.3 bedaquiline
rifampicin
mtrB 3627139 c.-526T>C upstream_gene_variant 0.26 bedaquiline
rifampicin
mtrB 3627143 c.-530G>C upstream_gene_variant 0.26 bedaquiline
rifampicin
mtrB 3627149 c.-536G>A upstream_gene_variant 0.29 bedaquiline
rifampicin
rpoA 3877587 c.921A>G synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3877593 c.915C>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3877614 c.894G>A synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoA 3877620 c.888G>A synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3877638 c.870T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoA 3877656 c.852T>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoA 3877665 c.843C>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoA 3877677 c.831G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoA 3877680 c.828G>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoA 3877686 c.822A>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoA 3877737 c.771G>C synonymous_variant 0.33 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoA 3877773 c.735G>C synonymous_variant 0.35 rifampicin
rpoA 3877776 c.732T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoA 3877797 c.711G>A synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.21 rifampicin
rpoA 3877875 c.633T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3877905 c.603A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3877908 c.600T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3877920 c.588G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3878259 c.249G>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoA 3878271 c.237T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoA 3878283 p.Glu75Asp missense_variant 0.48 rifampicin Uncertain significance
rpoA 3878292 c.216T>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoA 3878298 c.210A>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoA 3878301 c.207C>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoA 3878310 c.198G>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoA 3878313 c.195G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoA 3878343 c.165C>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.38 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 0.23 rifampicin
rpoA 3878367 c.141C>G synonymous_variant 0.22 rifampicin
rpoA 3878373 c.135G>C synonymous_variant 0.2 rifampicin
clpC1 4038767 c.1938G>T synonymous_variant 0.16 pyrazinamide
clpC1 4038770 c.1935C>T synonymous_variant 0.16 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.17 pyrazinamide
clpC1 4038782 c.1923G>T synonymous_variant 0.15 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038795 p.Ser637Thr missense_variant 0.14 pyrazinamide
clpC1 4038812 c.1893T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038815 c.1890G>T synonymous_variant 0.14 pyrazinamide
clpC1 4038842 c.1863G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038845 c.1858_1860delTCGinsAGC synonymous_variant 0.15 pyrazinamide
clpC1 4038860 c.1845G>T synonymous_variant 0.18 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
clpC1 4039094 c.1611C>T synonymous_variant 0.44 pyrazinamide Not assoc w R - Interim
clpC1 4039097 c.1608G>T synonymous_variant 0.44 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.53 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.53 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.5 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.46 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.46 pyrazinamide
clpC1 4039165 c.1540C>T synonymous_variant 0.32 pyrazinamide
clpC1 4039169 p.Glu512Asp missense_variant 0.32 pyrazinamide
clpC1 4039172 c.1533A>G synonymous_variant 0.3 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.32 pyrazinamide
clpC1 4039183 c.1522T>C synonymous_variant 0.32 pyrazinamide
clpC1 4039190 c.1515C>T synonymous_variant 0.27 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.32 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.32 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.33 pyrazinamide Uncertain significance
clpC1 4039472 c.1233G>C synonymous_variant 0.33 pyrazinamide
clpC1 4039478 c.1227G>C synonymous_variant 0.32 pyrazinamide
clpC1 4039481 c.1224T>C synonymous_variant 0.38 pyrazinamide
clpC1 4039487 c.1218G>C synonymous_variant 0.38 pyrazinamide
clpC1 4039522 c.1183C>T synonymous_variant 0.47 pyrazinamide
clpC1 4039528 c.1177C>A synonymous_variant 0.5 pyrazinamide
clpC1 4039541 c.1164C>G synonymous_variant 0.56 pyrazinamide
clpC1 4039544 c.1161C>T synonymous_variant 0.57 pyrazinamide
clpC1 4039556 c.1149G>C synonymous_variant 0.52 pyrazinamide
clpC1 4039559 c.1146C>G synonymous_variant 0.52 pyrazinamide
clpC1 4039565 c.1140G>T synonymous_variant 0.48 pyrazinamide
clpC1 4039570 p.Met379Leu missense_variant 0.46 pyrazinamide Uncertain significance
clpC1 4039574 p.Ala377Gly missense_variant 0.44 pyrazinamide
clpC1 4039586 c.1119G>C synonymous_variant 0.46 pyrazinamide
clpC1 4039601 c.1104G>A synonymous_variant 0.45 pyrazinamide
clpC1 4039610 c.1095G>C synonymous_variant 0.45 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.45 pyrazinamide
clpC1 4039622 c.1083C>T synonymous_variant 0.43 pyrazinamide
clpC1 4039661 c.1044T>C synonymous_variant 0.42 pyrazinamide
clpC1 4039694 c.1011G>C synonymous_variant 0.36 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.38 pyrazinamide
clpC1 4039913 c.792C>T synonymous_variant 0.38 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.42 pyrazinamide
clpC1 4039934 c.771G>C synonymous_variant 0.31 pyrazinamide
clpC1 4039943 c.762G>C synonymous_variant 0.31 pyrazinamide
clpC1 4039946 c.759A>G synonymous_variant 0.3 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.24 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039964 c.741C>G synonymous_variant 0.28 pyrazinamide
clpC1 4039975 p.Asp244Asn missense_variant 0.29 pyrazinamide Uncertain significance
clpC1 4039979 c.726C>G synonymous_variant 0.29 pyrazinamide
clpC1 4039982 c.723G>A synonymous_variant 0.35 pyrazinamide Not assoc w R - Interim
clpC1 4040009 c.696C>G synonymous_variant 0.41 pyrazinamide
clpC1 4040015 c.690G>C synonymous_variant 0.41 pyrazinamide
clpC1 4040021 c.684A>T synonymous_variant 0.39 pyrazinamide
clpC1 4040024 c.681A>G synonymous_variant 0.44 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.38 pyrazinamide
clpC1 4040048 c.657C>T synonymous_variant 0.43 pyrazinamide Not assoc w R - Interim
clpC1 4040087 c.618G>C synonymous_variant 0.38 pyrazinamide
clpC1 4040090 c.613_615delTCTinsAGC synonymous_variant 0.38 pyrazinamide
clpC1 4040093 c.612C>G synonymous_variant 0.39 pyrazinamide Not assoc w R - Interim
clpC1 4040126 c.579C>T synonymous_variant 0.33 pyrazinamide Not assoc w R - Interim
clpC1 4040495 c.210C>T synonymous_variant 0.35 pyrazinamide
clpC1 4040522 c.183T>C synonymous_variant 0.31 pyrazinamide Not assoc w R - Interim
clpC1 4040531 c.174T>G synonymous_variant 0.31 pyrazinamide
clpC1 4040540 c.165G>T synonymous_variant 0.31 pyrazinamide
clpC1 4040546 c.159G>C synonymous_variant 0.26 pyrazinamide
clpC1 4040558 c.147G>C synonymous_variant 0.26 pyrazinamide
clpC1 4040561 c.144A>G synonymous_variant 0.26 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.8 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
glpK 4138643 c.1113A>G synonymous_variant 0.25 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4138664 c.1092G>C synonymous_variant 0.28 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240756 c.894G>C synonymous_variant 0.2 ethambutol
embC 4240771 c.909G>C synonymous_variant 0.2 ethambutol
embC 4240772 p.Ser304Ala missense_variant 0.21 ethambutol
embC 4240778 p.His306Gly missense_variant 0.21 ethambutol
embC 4240781 p.Ala307Ser missense_variant 0.21 ethambutol Uncertain significance
embC 4240789 c.927T>C synonymous_variant 0.24 ethambutol
embC 4240819 c.957A>C synonymous_variant 0.3 ethambutol
embC 4240826 p.Ala322Ser missense_variant 0.29 ethambutol
embC 4240831 c.969T>G synonymous_variant 0.29 ethambutol
embC 4240856 c.994_996delGCGinsAC frameshift_variant&missense_variant 0.26 ethambutol
embC 4240859 c.997_999delCTGinsAC frameshift_variant&missense_variant 0.24 ethambutol
embC 4240876 c.1014C>T synonymous_variant 0.21 ethambutol
embC 4240879 c.1017G>T synonymous_variant 0.22 ethambutol
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
ethA 4328212 c.-740delC upstream_gene_variant 1.0 ethionamide
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