TB-Profiler result

Run: ERR11082350
Summary

Run ID: ERR11082350

Sample name:

Date: 2024-04-15T01:18:59.180866

Number of reads: 3497294

Percentage reads mapped: 97.04

Median coverage: 105.0

Strain: lineage4.6.2.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.99
lineage4.6.2 Euro-American RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) RD726 1.0
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin gid c.115delC Assoc w R
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
rpoB 761110 p.Asp435Val missense_variant 0.97 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin 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 8619 c.1318T>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620271 c.381C>G synonymous_variant 0.12 capreomycin
amikacin
kanamycin
ccsA 620307 c.417C>G synonymous_variant 0.13 capreomycin
amikacin
kanamycin
ccsA 620317 c.427_429delGTCinsCG frameshift_variant&missense_variant 0.15 capreomycin
amikacin
kanamycin
ccsA 620343 c.453G>C synonymous_variant 0.15 capreomycin
amikacin
kanamycin
ccsA 620712 c.822G>C synonymous_variant 0.13 capreomycin
amikacin
kanamycin
rpoB 760101 c.295T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760916 c.1110C>G synonymous_variant 0.16 rifampicin
rpoB 760919 c.1113C>G synonymous_variant 0.16 rifampicin
rpoB 760925 c.1119T>C synonymous_variant 0.14 rifampicin
rpoB 760928 c.1122G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760931 c.1125C>G synonymous_variant 0.15 rifampicin
rpoB 760937 c.1131G>A synonymous_variant 0.16 rifampicin
rpoB 760946 c.1140A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760973 c.1167G>C synonymous_variant 0.15 rifampicin
rpoB 760982 c.1176G>T synonymous_variant 0.14 rifampicin
rpoB 760985 c.1179G>T synonymous_variant 0.14 rifampicin
rpoB 760991 c.1185G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762167 c.2361T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.17 rifampicin
rpoC 763792 p.Glu141Asp missense_variant 0.14 rifampicin
rpoC 763851 p.Ala161Gly missense_variant 0.14 rifampicin
rpoC 763855 c.486C>T synonymous_variant 0.14 rifampicin
rpoC 763858 c.489A>G synonymous_variant 0.14 rifampicin
rpoC 763872 p.Gly168Ala missense_variant 0.16 rifampicin
rpoC 763876 p.Glu169Asp missense_variant 0.16 rifampicin
rpoC 763879 c.510A>G synonymous_variant 0.16 rifampicin
rpoC 763888 c.519G>C synonymous_variant 0.16 rifampicin
rpoC 763891 c.522G>C synonymous_variant 0.16 rifampicin
rpoC 763894 c.525A>G synonymous_variant 0.17 rifampicin
rpoC 763936 c.567C>G synonymous_variant 0.18 rifampicin
rpoC 763939 c.570G>A synonymous_variant 0.18 rifampicin
rpoC 763951 c.582G>A synonymous_variant 0.19 rifampicin
rpoC 763963 c.594C>G synonymous_variant 0.2 rifampicin
rpoC 763967 p.Gly200Ser missense_variant 0.18 rifampicin
rpoC 763972 c.603C>T synonymous_variant 0.18 rifampicin
rpoC 763987 c.618C>T synonymous_variant 0.19 rifampicin
rpoC 763996 c.627T>C synonymous_variant 0.21 rifampicin
rpoC 764005 c.636G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764011 c.642T>C synonymous_variant 0.23 rifampicin
rpoC 764024 c.655T>C synonymous_variant 0.21 rifampicin
rpoC 764040 p.Ser224Thr missense_variant 0.2 rifampicin
rpoC 764044 c.675T>G synonymous_variant 0.19 rifampicin
rpoC 764059 c.690G>T synonymous_variant 0.22 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.25 rifampicin
rpoC 764098 c.729A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764101 c.732C>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764140 c.771C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764159 c.790C>T synonymous_variant 0.24 rifampicin
rpoC 764188 c.819A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764195 p.Ser276Ile missense_variant 0.24 rifampicin
rpoC 764215 c.846A>C synonymous_variant 0.19 rifampicin
rpoC 764218 c.849C>T synonymous_variant 0.19 rifampicin
rpoC 764858 c.1489T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764887 c.1518G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764896 c.1527C>T synonymous_variant 0.15 rifampicin
rpoC 764902 c.1533C>T synonymous_variant 0.16 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.16 rifampicin
rpoC 764923 c.1554A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764932 c.1563C>G synonymous_variant 0.15 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765811 c.2442T>G synonymous_variant 0.14 rifampicin
rpoC 765814 c.2445A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765826 c.2457T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765835 c.2466C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 765883 c.2514C>G synonymous_variant 0.2 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.2 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 765934 c.2565C>T synonymous_variant 0.16 rifampicin
rpoC 766315 c.2946C>G synonymous_variant 0.15 rifampicin
rpoC 766321 c.2952C>G synonymous_variant 0.17 rifampicin
rpoC 766348 c.2979A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766369 c.3000C>G synonymous_variant 0.15 rifampicin
rpoC 766381 c.3012C>T synonymous_variant 0.17 rifampicin
rpoC 766384 c.3015A>G synonymous_variant 0.19 rifampicin
rpoC 766393 c.3024C>G synonymous_variant 0.21 rifampicin
rpoC 766402 c.3033C>G synonymous_variant 0.23 rifampicin
rpoC 766408 c.3039C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 766426 c.3057C>T synonymous_variant 0.2 rifampicin
rpoC 766456 c.3087C>G synonymous_variant 0.15 rifampicin
rpoC 766573 c.3204T>C synonymous_variant 0.17 rifampicin
rpoC 766585 c.3216T>C synonymous_variant 0.18 rifampicin
rpoC 766594 c.3225G>C synonymous_variant 0.18 rifampicin
rpoC 766607 p.Ile1080Leu missense_variant 0.2 rifampicin
rpoC 766630 c.3261G>T synonymous_variant 0.22 rifampicin
rpoC 766660 c.3291G>A synonymous_variant 0.24 rifampicin
rpoC 766666 c.3297C>G synonymous_variant 0.22 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.21 rifampicin
rpoC 766700 c.3331C>T synonymous_variant 0.16 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.16 rifampicin
rpoC 766733 c.3364C>T synonymous_variant 0.16 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.15 rifampicin
rpoC 766741 c.3372G>C synonymous_variant 0.16 rifampicin
rpoC 766750 c.3381C>G synonymous_variant 0.16 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.15 rifampicin
rpoC 766996 c.3627C>G synonymous_variant 0.21 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778298 c.183G>A synonymous_variant 1.0 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1303545 c.615A>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303575 c.645G>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303584 c.654C>G synonymous_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1303596 c.666G>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303605 c.675C>G synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303614 c.684C>T synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fbiC 1303617 c.687C>G synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303629 c.699C>T synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303632 c.702T>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475487 n.1830C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475999 n.2342G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
inhA 1674765 c.564C>T synonymous_variant 0.12 ethionamide
isoniazid
inhA 1674792 c.591G>C synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674801 c.600T>C synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674846 p.Ile215Met missense_variant 0.13 ethionamide
isoniazid
rpsA 1833703 c.162C>T synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1833724 c.183C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833760 c.219C>T synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1833790 c.249T>C synonymous_variant 0.15 pyrazinamide
rpsA 1833793 c.252C>T synonymous_variant 0.15 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.14 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833859 c.318C>T synonymous_variant 0.14 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.15 pyrazinamide
rpsA 1833895 c.354G>C synonymous_variant 0.19 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.19 pyrazinamide
rpsA 1833970 c.429G>A synonymous_variant 0.19 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.16 pyrazinamide
tsnR 1853420 c.-186T>G upstream_gene_variant 0.15 linezolid
tsnR 1853429 c.-177G>C upstream_gene_variant 0.16 linezolid
tsnR 1853441 c.-165C>G upstream_gene_variant 0.16 linezolid
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
bacA 2063187 c.1542C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2155389 c.723C>G synonymous_variant 1.0 isoniazid Not assoc w R
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.98 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2517941 c.-174C>G upstream_gene_variant 0.14 isoniazid
kasA 2517950 c.-165C>G upstream_gene_variant 0.14 isoniazid
kasA 2517962 c.-153C>G upstream_gene_variant 0.14 isoniazid
Rv2477c 2783572 c.471A>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783605 c.438T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783788 c.255T>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783794 c.249G>A synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783797 p.Asp82Glu missense_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783806 c.237G>C synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783821 p.Gln74Leu missense_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783827 c.216C>T synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783833 c.210G>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783836 c.207C>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783843 p.Gly67Asp missense_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783846 p.Thr66Asn missense_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783857 c.186C>G synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783860 c.183T>C synonymous_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783881 c.160_162delTTGinsCC frameshift_variant&missense_variant 0.15 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2477c 2783884 c.159T>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783920 c.123G>T synonymous_variant 0.27 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin Not assoc w R - Interim
amikacin
Rv2477c 2783938 c.105T>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783956 p.Tyr29Phe missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783968 c.75G>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783971 c.72G>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783980 c.63C>G synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783992 c.51T>C synonymous_variant 0.15 ethambutol Not assoc w R - Interim
moxifloxacin
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
Rv2680 2996208 p.Ala35Asp missense_variant 1.0 capreomycin Uncertain significance
thyX 3067474 p.Pro158Ala missense_variant 0.96 para-aminosalicylic_acid
Rv3083 3448567 p.His22Asp missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3612571 c.546C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
lpqB 3624739 p.Ala58Ser missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrA 3626825 c.525T>A synonymous_variant 0.13 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626924 c.-311G>C upstream_gene_variant 0.12 bedaquiline
rifampicin
mtrB 3626927 c.-314G>C upstream_gene_variant 0.12 bedaquiline
rifampicin
mtrB 3626930 c.-317A>G upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626933 c.-320C>T upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626942 c.-329A>C upstream_gene_variant 0.16 bedaquiline
rifampicin
rpoA 3877613 p.Ile299Val missense_variant 0.15 rifampicin
rpoA 3877617 c.891G>C synonymous_variant 0.15 rifampicin
rpoA 3877638 c.870T>G synonymous_variant 0.17 rifampicin
rpoA 3877656 c.852T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.14 rifampicin
rpoA 3877677 c.831G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877680 c.828G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877686 c.822A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877707 c.801G>A synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877737 c.771G>C synonymous_variant 0.18 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3877758 c.750G>C synonymous_variant 0.17 rifampicin
rpoA 3877764 c.744C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877815 c.693C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877989 c.519A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878001 c.507A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878022 c.486T>C synonymous_variant 0.21 rifampicin
rpoA 3878025 c.483C>T synonymous_variant 0.22 rifampicin
rpoA 3878028 c.480G>C synonymous_variant 0.21 rifampicin
rpoA 3878031 c.477T>C synonymous_variant 0.22 rifampicin
rpoA 3878043 c.465G>C synonymous_variant 0.24 rifampicin
rpoA 3878046 c.462T>G synonymous_variant 0.24 rifampicin
rpoA 3878055 c.453A>G synonymous_variant 0.27 rifampicin
rpoA 3878061 c.447G>C synonymous_variant 0.26 rifampicin
rpoA 3878067 c.441C>G synonymous_variant 0.26 rifampicin
rpoA 3878070 c.438T>C synonymous_variant 0.26 rifampicin
rpoA 3878094 c.414C>G synonymous_variant 0.27 rifampicin
rpoA 3878103 c.405A>G synonymous_variant 0.26 rifampicin
rpoA 3878106 c.402G>C synonymous_variant 0.25 rifampicin
rpoA 3878118 c.390T>C synonymous_variant 0.25 rifampicin
rpoA 3878130 c.378C>G synonymous_variant 0.24 rifampicin
rpoA 3878145 c.363C>G synonymous_variant 0.22 rifampicin
rpoA 3878163 c.345C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878166 c.342C>G synonymous_variant 0.19 rifampicin
rpoA 3878169 c.339G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3878184 c.324C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878187 c.321C>G synonymous_variant 0.18 rifampicin
rpoA 3878193 c.315T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878217 c.291A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878256 c.252G>C synonymous_variant 0.13 rifampicin
rpoA 3878298 c.210A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>C synonymous_variant 0.15 rifampicin
rpoA 3878313 c.195G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>C synonymous_variant 0.17 rifampicin
rpoA 3878334 c.174T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.21 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 0.18 rifampicin
rpoA 3878370 c.138T>C synonymous_variant 0.22 rifampicin
rpoA 3878376 c.132G>C synonymous_variant 0.22 rifampicin
rpoA 3878384 c.124C>T synonymous_variant 0.21 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.21 rifampicin
rpoA 3878391 c.117T>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoA 3878415 c.93C>T synonymous_variant 0.19 rifampicin
rpoA 3878418 c.90C>T synonymous_variant 0.19 rifampicin
rpoA 3878436 c.72A>G synonymous_variant 0.16 rifampicin
rpoA 3878442 c.66G>C synonymous_variant 0.16 rifampicin
rpoA 3878454 c.54A>G synonymous_variant 0.15 rifampicin
rpoA 3878458 p.Asn17Ser missense_variant 0.15 rifampicin
clpC1 4038508 c.2197C>T synonymous_variant 0.14 pyrazinamide
clpC1 4038518 c.2187G>T synonymous_variant 0.14 pyrazinamide
clpC1 4038596 c.2109A>G synonymous_variant 0.17 pyrazinamide
clpC1 4038620 c.2085G>A synonymous_variant 0.16 pyrazinamide
clpC1 4038623 c.2082A>G synonymous_variant 0.17 pyrazinamide
clpC1 4038653 c.2052C>T synonymous_variant 0.17 pyrazinamide
clpC1 4038658 p.Lys683Gln missense_variant 0.14 pyrazinamide
clpC1 4038661 p.Ser682Thr missense_variant 0.13 pyrazinamide
clpC1 4038662 c.2043T>C synonymous_variant 0.13 pyrazinamide
clpC1 4038668 c.2037G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038671 c.2034T>C synonymous_variant 0.12 pyrazinamide
clpC1 4038677 c.2028G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4038692 c.2013C>G synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 0.13 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 0.13 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038809 c.1896G>A synonymous_variant 0.14 pyrazinamide
clpC1 4038812 c.1893T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038875 c.1830C>G synonymous_variant 0.14 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.15 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.15 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.17 pyrazinamide
clpC1 4038941 c.1764G>A synonymous_variant 0.17 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.13 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.13 pyrazinamide
clpC1 4040291 c.414G>C synonymous_variant 0.12 pyrazinamide
glpK 4138670 c.1086G>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138681 p.Met359Val missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138682 c.1074C>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138702 p.Gln352Glu missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242550 c.2688C>G synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245745 p.Pro838Leu missense_variant 1.0 ethambutol Uncertain significance
embB 4247527 c.1014G>C synonymous_variant 0.13 ethambutol
embB 4247554 c.1041T>C synonymous_variant 0.14 ethambutol
embB 4247566 c.1053C>G synonymous_variant 0.13 ethambutol
aftB 4267272 p.Lys522Arg missense_variant 1.0 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
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