TB-Profiler result

Run: ERR4799989
Summary

Run ID: ERR4799989

Sample name:

Date: 2024-10-05T12:38:50.731253

Number of reads: 2246188

Percentage reads mapped: 74.11

Median coverage: 57.0

Strain: lineage2.2.1.2

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
lineage2 East-Asian RD105 0.96
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.96
lineage2.2 East-Asian (Beijing) RD105;RD207 0.98
lineage2.2.1.2 East-Asian (Beijing) RD105;RD207;RD181;RD142 0.95
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Ala171Val Uncertain significance Mutation from literature
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
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 7582 p.Asp94Gly missense_variant 0.92 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.74 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.78 streptomycin Assoc w R
inhA 1673432 c.-770T>C upstream_gene_variant 0.93 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288730 p.Ala171Val missense_variant 0.95 pyrazinamide Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.98 ethambutol 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 6598 c.-704C>G upstream_gene_variant 0.13 levofloxacin
moxifloxacin
gyrA 6610 c.-692C>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6613 c.-689A>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6616 c.-686A>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6622 c.-680C>T upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6631 c.-671C>T upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 6634 c.-668T>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6637 c.-665T>G upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6640 c.-662A>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6643 c.-659A>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6646 c.-656C>T upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrA 6655 c.-647T>C upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 6673 c.-629A>C upstream_gene_variant 0.18 levofloxacin
moxifloxacin
gyrA 6676 c.-626T>G upstream_gene_variant 0.18 levofloxacin
moxifloxacin
gyrA 6700 c.-602T>C upstream_gene_variant 0.2 levofloxacin
moxifloxacin
gyrA 6703 c.-599G>C upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 6709 c.-593A>G upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 6712 c.-590G>C upstream_gene_variant 0.13 levofloxacin
moxifloxacin
gyrA 6724 c.-578G>C upstream_gene_variant 0.12 levofloxacin
moxifloxacin
gyrA 6730 c.-572A>G upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6742 c.-560A>G upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 6751 c.-551G>C upstream_gene_variant 0.13 levofloxacin
moxifloxacin
gyrA 6775 c.-527G>T upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 7084 c.-218A>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrB 7100 c.1861T>C synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.99 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.98 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.95 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.97 ethionamide Uncertain significance
rpoB 761027 c.1221A>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761051 c.1245G>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 761063 c.1257C>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761171 c.1365C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761198 c.1392G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761213 c.1407G>C synonymous_variant 0.28 rifampicin
rpoB 761217 p.Pro471Ser missense_variant 0.26 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761258 c.1452G>A synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761264 c.1458C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 761555 c.1749G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761558 c.1752C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761570 c.1764T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761600 c.1794T>C synonymous_variant 0.2 rifampicin
rpoB 761612 c.1806G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761627 c.1821C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.15 rifampicin
rpoB 761666 c.1860G>C synonymous_variant 0.13 rifampicin
rpoB 762959 c.3153G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762995 c.3189G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763053 c.3247T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 763088 c.3282C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 763094 c.3288G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763127 c.3321G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763142 c.-228C>G upstream_gene_variant 0.17 rifampicin
rpoB 763157 c.3351G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763166 c.3360A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763172 c.3366G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763468 c.99G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763495 c.126G>A synonymous_variant 0.15 rifampicin
rpoC 763589 p.Ile74Val missense_variant 0.14 rifampicin
rpoC 763642 c.273G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763669 c.300C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764557 c.1188C>T synonymous_variant 0.15 rifampicin
rpoC 764575 c.1206T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764605 c.1236G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764623 c.1254C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764692 c.1323C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764701 c.1332C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764713 c.1344G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764797 c.1428G>C synonymous_variant 0.26 rifampicin
rpoC 764803 c.1434C>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.26 rifampicin Not assoc w R
rpoC 764815 c.1446A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764817 p.Val483Gly missense_variant 0.69 rifampicin Uncertain significance
rpoC 764827 c.1458G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 766291 c.2922G>C synonymous_variant 0.13 rifampicin
rpoC 766297 c.2928G>C synonymous_variant 0.13 rifampicin
rpoC 767134 c.3765C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 767138 c.3769C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767149 c.3780C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767155 c.3786C>G synonymous_variant 0.13 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.94 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.96 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781628 c.69T>G synonymous_variant 0.13 streptomycin
rpsL 781658 c.99A>G synonymous_variant 0.17 streptomycin
rpsL 781682 c.123T>C synonymous_variant 0.19 streptomycin
rpsL 781685 c.126G>C synonymous_variant 0.19 streptomycin
rpsL 781706 c.147T>G synonymous_variant 0.19 streptomycin
rpsL 781709 c.150G>C synonymous_variant 0.18 streptomycin Not assoc w R - Interim
rpsL 781715 c.156T>C synonymous_variant 0.18 streptomycin
rpsL 781721 c.162C>T synonymous_variant 0.17 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.16 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.15 streptomycin
rplC 800612 c.-197A>G upstream_gene_variant 0.15 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.18 linezolid
rplC 800633 c.-176T>C upstream_gene_variant 0.22 linezolid
rplC 800645 c.-164C>G upstream_gene_variant 0.22 linezolid
rplC 800648 c.-161A>T upstream_gene_variant 0.21 linezolid
rplC 800651 c.-158G>C upstream_gene_variant 0.22 linezolid
rplC 800678 c.-131C>T upstream_gene_variant 0.2 linezolid
rplC 800684 c.-125G>A upstream_gene_variant 0.2 linezolid
rplC 800690 c.-119C>T upstream_gene_variant 0.2 linezolid
rplC 800693 c.-116A>C upstream_gene_variant 0.19 linezolid
rplC 800702 c.-107G>C upstream_gene_variant 0.19 linezolid
rplC 800703 c.-106_-104delTTGinsCTT upstream_gene_variant 0.17 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.19 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.19 linezolid
rplC 800744 c.-65G>C upstream_gene_variant 0.13 linezolid
rplC 800747 c.-62C>G upstream_gene_variant 0.13 linezolid
rplC 800759 c.-50C>T upstream_gene_variant 0.13 linezolid
rplC 800768 c.-41C>G upstream_gene_variant 0.14 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.97 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471922 n.78delT non_coding_transcript_exon_variant 0.41 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1471931 n.87delA non_coding_transcript_exon_variant 0.4 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.4 kanamycin
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472019 n.174G>A non_coding_transcript_exon_variant 0.48 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472031 n.186G>C non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472033 n.188A>C non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472035 n.190G>T non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472040 n.195T>G non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472041 n.196C>T non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472042 n.197T>G non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.51 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.49 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472672 n.830delT non_coding_transcript_exon_variant 0.42 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472848 n.1003T>G non_coding_transcript_exon_variant 0.38 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472850 n.1005T>C non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472859 n.1014G>C non_coding_transcript_exon_variant 0.38 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.44 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.53 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTC non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.65 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.57 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.6 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.58 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473717 n.60G>A non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473731 n.74T>A non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473743 n.86C>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473797 n.140G>T non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473812 n.155G>A non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid
rrl 1473815 n.158T>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1473829 n.172G>T non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474287 n.630_632delTCCinsCTCG non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1474293 n.636T>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1474294 n.638_649delCTCTCCGGAGGA non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475487 n.1830C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1475760 n.2103_2107delCCGCAinsTCCTTCG non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.36 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475989 n.2332T>A non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476030 n.2373_2378delACCTCGinsGCGCAC non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476088 n.2431A>T non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.45 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1476105 n.2448G>C non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1476114 n.2457T>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.55 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.45 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476665 n.3008T>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid
rrl 1476666 n.3009C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1476723 n.3066T>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476731 n.3074G>A non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476732 n.3075T>C non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476741 n.3084G>C non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476743 n.3086A>C non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476744 n.3087G>A non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476746 n.3089T>C non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476750 n.3093T>C non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1476758 n.3101G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476770 n.3113T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476771 n.3114G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rpsA 1833829 c.288A>G synonymous_variant 0.16 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.16 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.18 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.18 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.17 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.19 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.96 pyrazinamide Not assoc w R - Interim
rpsA 1834396 c.855G>C synonymous_variant 0.22 pyrazinamide
rpsA 1834408 c.867C>T synonymous_variant 0.2 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834423 c.882G>T synonymous_variant 0.21 pyrazinamide
rpsA 1834432 c.891G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.28 pyrazinamide
rpsA 1834483 c.942G>A synonymous_variant 0.26 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.22 pyrazinamide
rpsA 1834520 p.Ala327Ser missense_variant 0.2 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834543 c.1002C>G synonymous_variant 0.18 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834554 c.1014_1015delTG frameshift_variant 0.18 pyrazinamide Uncertain significance
rpsA 1834558 c.1017_1018insAG frameshift_variant 0.19 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.97 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 1.0 isoniazid Not assoc w R
katG 2156475 c.-364A>G upstream_gene_variant 0.95 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.97 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.98 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878244 c.264G>A synonymous_variant 0.14 rifampicin
clpC1 4038953 c.1752A>G synonymous_variant 0.14 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039079 c.1626C>G synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4039364 c.1341C>A synonymous_variant 0.17 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039904 c.801A>G synonymous_variant 0.17 pyrazinamide
clpC1 4039907 c.798G>A synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039931 c.774T>C synonymous_variant 0.18 pyrazinamide
clpC1 4039934 c.771G>C synonymous_variant 0.18 pyrazinamide
clpC1 4039946 c.759A>T synonymous_variant 0.15 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039991 c.714G>C synonymous_variant 0.16 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.95 ethambutol Not assoc w R
ethA 4327415 p.Ala20Val missense_variant 0.95 ethionamide Uncertain significance
whiB6 4338242 p.Gln94* stop_gained 0.98 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.98 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.96 streptomycin Not assoc w R