TB-Profiler result

Run: SRR1173218
Summary

Run ID: SRR1173218

Sample name:

Date: 2024-04-15T17:06:10.156874

Number of reads: 548907

Percentage reads mapped: 64.17

Median coverage: 12.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.92
lineage4.3.3 Euro-American (LAM) RD115 0.98
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA c.456dupC Assoc w R
streptomycin rrs n.462C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA c.-11A>G Uncertain significance Mutation from literature
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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance Mutation from literature
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.63 amikacin Assoc w R
kanamycin Assoc w R
capreomycin Assoc w R
pncA 2288785 c.456dupC frameshift_variant 1.0 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.82 ethambutol Assoc w R
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide Uncertain significance Mutation from literature
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 1254 c.1254T>C synonymous_variant 0.38 isoniazid
dnaA 1278 c.1278T>C synonymous_variant 0.41 isoniazid
dnaA 1284 c.1284C>G synonymous_variant 0.47 isoniazid
gyrB 6292 c.1053G>C synonymous_variant 0.33 levofloxacin
moxifloxacin
gyrB 6307 c.1068T>G synonymous_variant 0.35 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6518 p.Val427Met missense_variant 0.86 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 8040 p.Gly247Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9284 c.1983T>C synonymous_variant 0.5 levofloxacin
moxifloxacin
gyrA 9291 c.1990C>T synonymous_variant 0.5 levofloxacin
moxifloxacin
gyrA 9296 c.1995T>C synonymous_variant 0.53 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
gyrA 9308 p.Asp669Glu missense_variant 0.47 levofloxacin
moxifloxacin
gyrA 9323 c.2022C>G synonymous_variant 0.44 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9335 c.2034G>C synonymous_variant 0.36 levofloxacin
moxifloxacin
fgd1 490827 c.45C>T synonymous_variant 0.53 clofazimine
pretomanid
delamanid
fgd1 490848 c.66A>G synonymous_variant 0.44 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fgd1 490851 c.69A>T synonymous_variant 0.44 clofazimine
pretomanid
delamanid
fgd1 490868 p.Ala29Gly missense_variant 0.39 clofazimine
pretomanid
delamanid
ccsA 619609 c.-282G>C upstream_gene_variant 0.35 capreomycin
amikacin
kanamycin
Rv0565c 657300 c.171C>G synonymous_variant 0.29 ethionamide
hadA 731747 c.-183T>C upstream_gene_variant 0.27 isoniazid
hadA 731774 c.-156T>C upstream_gene_variant 0.35 isoniazid
hadA 731789 c.-141A>G upstream_gene_variant 0.4 isoniazid
hadA 731792 c.-138G>A upstream_gene_variant 0.42 isoniazid
hadA 731801 c.-129C>G upstream_gene_variant 0.4 isoniazid
hadA 732396 p.Gly156Ala missense_variant 0.54 isoniazid
hadA 732398 p.Ala157Thr missense_variant 0.54 isoniazid
nusG 734442 c.189G>A synonymous_variant 0.54 rifampicin
nusG 734451 c.198G>C synonymous_variant 0.53 rifampicin
nusG 734457 c.204C>G synonymous_variant 0.47 rifampicin
rpoB 760283 c.477G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoB 760307 c.501T>C synonymous_variant 0.31 rifampicin
rpoB 760310 c.504G>C synonymous_variant 0.33 rifampicin
rpoB 760328 c.522G>C synonymous_variant 0.4 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.39 rifampicin
rpoB 760361 c.555T>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 760370 c.564C>G synonymous_variant 0.4 rifampicin
rpoB 760376 p.Asp190Glu missense_variant 0.35 rifampicin Uncertain significance
rpoB 760380 p.Thr192Leu missense_variant 0.33 rifampicin
rpoB 760472 c.666C>T synonymous_variant 0.53 rifampicin
rpoB 760475 c.669A>G synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoB 760541 c.735G>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 760547 c.741G>C synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoB 760563 p.Arg253Met missense_variant 0.42 rifampicin Uncertain significance
rpoB 760591 p.Val262Ala missense_variant 0.53 rifampicin
rpoB 760611 c.805T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 760655 c.849A>G synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.47 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 760805 c.999G>C synonymous_variant 0.41 rifampicin
rpoB 760817 c.1011A>G synonymous_variant 0.38 rifampicin
rpoB 760820 c.1014T>C synonymous_variant 0.38 rifampicin
rpoB 760869 p.Val355Ile missense_variant 0.27 rifampicin Uncertain significance
rpoB 761492 c.1686G>C synonymous_variant 0.32 rifampicin
rpoB 761510 c.1704T>C synonymous_variant 0.36 rifampicin
rpoB 761531 c.1725C>G synonymous_variant 0.39 rifampicin
rpoB 761537 c.1731C>G synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoB 761570 c.1764T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 0.5 rifampicin
rpoB 761612 c.1806G>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoB 761948 c.2142G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 762008 c.2202C>T synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>T synonymous_variant 0.55 rifampicin
rpoB 762017 c.2211A>G synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 762176 c.2370T>C synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.64 rifampicin Not assoc w R - Interim
rpoB 762206 c.2400C>G synonymous_variant 0.73 rifampicin
rpoB 762233 c.2427G>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoB 762246 c.2440C>T synonymous_variant 0.53 rifampicin
rpoB 762254 c.2448T>G synonymous_variant 0.5 rifampicin
rpoB 762257 c.2451C>G synonymous_variant 0.47 rifampicin
rpoB 762266 c.2460T>C synonymous_variant 0.53 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 763402 c.33C>G synonymous_variant 0.39 rifampicin
rpoC 763411 c.42T>G synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 763414 c.45T>C synonymous_variant 0.39 rifampicin
rpoC 763441 c.72C>T synonymous_variant 0.45 rifampicin
rpoC 763444 c.75T>C synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 763942 c.573C>G synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 763945 c.576T>C synonymous_variant 0.55 rifampicin
rpoC 763951 c.582G>C synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 763960 c.591T>C synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 764215 c.846A>G synonymous_variant 0.44 rifampicin
rpoC 764236 c.867G>A synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 764248 c.879C>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764257 c.888G>C synonymous_variant 0.53 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.53 rifampicin
rpoC 764269 c.900G>C synonymous_variant 0.5 rifampicin
rpoC 764272 c.903G>C synonymous_variant 0.53 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>C synonymous_variant 0.39 rifampicin
rpoC 764651 c.1282_1284delTCGinsAGC synonymous_variant 0.39 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.52 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765404 p.Leu679Val missense_variant 0.54 rifampicin
rpoC 765409 c.2040T>C synonymous_variant 0.5 rifampicin
rpoC 765421 c.2052C>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 765613 p.His748Gln missense_variant 0.5 rifampicin
rpoC 765625 c.2256C>G synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 765628 c.2259G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 765631 p.Asp754Glu missense_variant 0.47 rifampicin
rpoC 765883 c.2514C>G synonymous_variant 0.39 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.37 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 765937 c.2568T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 766483 c.3114G>C synonymous_variant 0.54 rifampicin
rpoC 766484 c.3115_3117delGTAinsAC frameshift_variant&missense_variant 0.54 rifampicin
rpoC 766492 c.3123T>C synonymous_variant 0.57 rifampicin
rpoC 766522 c.3153C>G synonymous_variant 0.6 rifampicin
rpoC 766528 c.3159T>C synonymous_variant 0.59 rifampicin
rpoC 766531 c.3162G>C synonymous_variant 0.53 rifampicin
rpoC 766540 p.Asp1057Glu missense_variant 0.53 rifampicin
rpoC 766549 c.3180G>C synonymous_variant 0.5 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.35 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.39 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.38 rifampicin
rpoC 766861 c.3492G>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.5 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.53 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.54 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.46 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.39 rifampicin
rpoC 767014 c.3645G>C synonymous_variant 0.36 rifampicin
rpoC 767134 c.3765C>A synonymous_variant 0.47 rifampicin
rpoC 767158 c.3789T>C synonymous_variant 0.59 rifampicin Not assoc w R - Interim
rpoC 767180 p.Ala1271Gln missense_variant 0.59 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoC 767206 c.3837C>G synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 767209 c.3840T>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 767212 c.3843G>C synonymous_variant 0.59 rifampicin
rpoC 767221 c.3852C>G synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoC 767230 c.3861G>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoC 767233 c.3864T>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
mmpL5 777170 c.1311T>C synonymous_variant 0.35 clofazimine
bedaquiline
rplC 800582 c.-227C>G upstream_gene_variant 0.5 linezolid
rplC 800612 c.-197A>G upstream_gene_variant 0.5 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.45 linezolid
rplC 800627 c.-182C>T upstream_gene_variant 0.42 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.5 linezolid
rplC 800693 c.-116A>G upstream_gene_variant 0.37 linezolid
fbiC 1304891 p.Ile654Thr missense_variant 0.64 clofazimine
pretomanid
delamanid
fbiC 1304893 p.Gly655Ser missense_variant 0.64 clofazimine
pretomanid
delamanid
fbiC 1304907 c.1977C>G synonymous_variant 0.62 clofazimine
pretomanid
delamanid
fbiC 1304910 c.1980G>C synonymous_variant 0.62 clofazimine
pretomanid
delamanid
fbiC 1304916 c.1986T>C synonymous_variant 0.69 clofazimine
pretomanid
delamanid
fbiC 1304928 c.1998T>C synonymous_variant 0.64 clofazimine
pretomanid
delamanid
fbiC 1304937 c.2007G>C synonymous_variant 0.65 clofazimine
pretomanid
delamanid
fbiC 1304958 c.2028T>G synonymous_variant 0.64 clofazimine
pretomanid
delamanid
fbiC 1304983 c.2053C>T synonymous_variant 0.6 clofazimine
pretomanid
delamanid
fbiC 1304994 c.2064A>G synonymous_variant 0.53 clofazimine
pretomanid
delamanid
fbiC 1304995 p.Leu689Met missense_variant 0.53 clofazimine
pretomanid
delamanid
fbiC 1305006 c.2076A>G synonymous_variant 0.47 clofazimine
pretomanid
delamanid
fbiC 1305012 c.2082G>C synonymous_variant 0.44 clofazimine
pretomanid
delamanid
fbiC 1305015 c.2085G>C synonymous_variant 0.44 clofazimine
pretomanid
delamanid
fbiC 1305021 c.2091C>G synonymous_variant 0.42 clofazimine
pretomanid
delamanid
fbiC 1305030 c.2100G>C synonymous_variant 0.39 clofazimine
pretomanid
delamanid
fbiC 1305033 c.2103T>G synonymous_variant 0.37 clofazimine
pretomanid
delamanid
atpE 1460816 c.-229T>C upstream_gene_variant 0.54 bedaquiline
atpE 1460831 c.-214T>C upstream_gene_variant 0.62 bedaquiline
atpE 1460840 c.-205A>G upstream_gene_variant 0.67 bedaquiline
atpE 1460852 c.-193C>G upstream_gene_variant 0.64 bedaquiline
atpE 1460855 c.-190T>C upstream_gene_variant 0.58 bedaquiline
atpE 1460858 c.-187C>G upstream_gene_variant 0.62 bedaquiline
atpE 1460861 c.-184C>G upstream_gene_variant 0.62 bedaquiline
atpE 1461170 c.126A>G synonymous_variant 0.62 bedaquiline
atpE 1461185 c.141G>T synonymous_variant 0.64 bedaquiline
atpE 1461197 c.153A>G synonymous_variant 0.65 bedaquiline
atpE 1461219 c.175T>C synonymous_variant 0.53 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471932 n.87A>G non_coding_transcript_exon_variant 0.39 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475267 n.1610G>A non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.93 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476105 n.2448_2449delGAinsT non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.56 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476732 n.3075T>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476733 n.3076C>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1476750 n.3093T>C non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476755 n.3098G>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
fabG1 1673710 p.Leu91Ile missense_variant 0.53 ethionamide
isoniazid
fabG1 1673716 p.Ala93Lys missense_variant 0.5 ethionamide
isoniazid
fabG1 1673733 p.Met98Ile missense_variant 0.56 ethionamide
isoniazid
inhA 1673748 c.-454A>G upstream_gene_variant 0.39 ethionamide
isoniazid
fabG1 1673749 p.Lys104Arg missense_variant 0.35 ethionamide
isoniazid
fabG1 1673758 p.Lys107Glu missense_variant 0.35 ethionamide
isoniazid
inhA 1674864 c.663C>T synonymous_variant 0.38 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
inhA 1674870 c.669T>C synonymous_variant 0.43 ethionamide
isoniazid
inhA 1674879 c.678T>C synonymous_variant 0.42 ethionamide
isoniazid
inhA 1674900 c.699G>A synonymous_variant 0.47 ethionamide
isoniazid
inhA 1674903 c.702T>C synonymous_variant 0.44 ethionamide
isoniazid
inhA 1674904 p.Ala235Pro missense_variant 0.41 ethionamide
isoniazid
inhA 1674909 c.708G>A synonymous_variant 0.44 ethionamide
isoniazid
inhA 1674942 c.741T>G synonymous_variant 0.32 ethionamide
isoniazid
rpsA 1833554 p.Thr5Ala missense_variant 0.32 pyrazinamide Uncertain significance
rpsA 1833568 c.27G>C synonymous_variant 0.32 pyrazinamide Not assoc w R - Interim
rpsA 1833589 c.48A>T synonymous_variant 0.42 pyrazinamide
rpsA 1833595 c.54T>C synonymous_variant 0.41 pyrazinamide
rpsA 1833661 c.120A>G synonymous_variant 0.54 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.55 pyrazinamide
rpsA 1833721 c.180A>G synonymous_variant 0.55 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.55 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.58 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.5 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.5 pyrazinamide
rpsA 1833748 c.207C>G synonymous_variant 0.56 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.56 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.5 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.53 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.56 pyrazinamide
rpsA 1833971 c.430C>T synonymous_variant 0.56 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.53 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.67 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.68 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.72 pyrazinamide
rpsA 1834195 c.654G>C synonymous_variant 0.4 pyrazinamide
rpsA 1834210 c.669C>T synonymous_variant 0.33 pyrazinamide
rpsA 1834222 c.681T>C synonymous_variant 0.35 pyrazinamide
rpsA 1834264 c.723G>C synonymous_variant 0.4 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.5 pyrazinamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2290009 c.-768A>G upstream_gene_variant 0.43 pyrazinamide
pncA 2290015 c.-774A>C upstream_gene_variant 0.4 pyrazinamide
kasA 2517950 c.-165C>G upstream_gene_variant 0.44 isoniazid
kasA 2517989 c.-126T>C upstream_gene_variant 0.33 isoniazid
kasA 2518609 p.Met165Ile missense_variant 0.33 isoniazid
kasA 2519122 c.1008G>C synonymous_variant 0.44 isoniazid
ahpC 2726303 c.111T>C synonymous_variant 0.44 isoniazid
ahpC 2726645 c.453C>G synonymous_variant 0.6 isoniazid
ahpC 2726657 c.465A>C synonymous_variant 0.65 isoniazid Not assoc w R - Interim
ahpC 2726669 p.Asp159Glu missense_variant 0.77 isoniazid
ahpC 2726672 c.480G>A synonymous_variant 0.83 isoniazid Not assoc w R - Interim
ahpC 2726675 c.483A>G synonymous_variant 0.83 isoniazid
ahpC 2726681 c.489A>C synonymous_variant 0.83 isoniazid Not assoc w R - Interim
ahpC 2726687 c.495C>G synonymous_variant 0.77 isoniazid
ahpC 2726693 c.501C>G synonymous_variant 0.77 isoniazid
ahpC 2726696 c.504C>G synonymous_variant 0.75 isoniazid
ahpC 2726717 c.525A>G synonymous_variant 0.58 isoniazid
Rv2477c 2782483 c.1560G>C synonymous_variant 0.43 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782513 c.1530G>T synonymous_variant 0.38 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782522 c.1521G>C synonymous_variant 0.35 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782528 c.1515G>C synonymous_variant 0.35 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783140 c.903C>G synonymous_variant 0.67 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783158 c.885A>C synonymous_variant 0.75 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
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 2783182 c.861C>G synonymous_variant 0.8 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783194 c.849A>G synonymous_variant 0.8 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783719 c.324A>G synonymous_variant 0.35 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625569 c.1045T>C synonymous_variant 0.44 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625572 p.Thr348Ser missense_variant 0.42 bedaquiline
rifampicin
lpqB 3625579 c.-669A>G upstream_gene_variant 0.44 bedaquiline
rifampicin
lpqB 3625749 c.-839C>T upstream_gene_variant 0.32 bedaquiline
rifampicin
mtrB 3625755 p.Ala287Thr missense_variant 0.37 bedaquiline
rifampicin Uncertain significance
mtrB 3625765 c.849C>G synonymous_variant 0.4 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626759 c.591T>C synonymous_variant 0.48 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626774 c.574_576delAGGinsCC frameshift_variant&missense_variant 0.47 bedaquiline
rifampicin
mtrB 3626783 c.-170C>G upstream_gene_variant 0.47 bedaquiline
rifampicin
mtrA 3626786 c.564A>G synonymous_variant 0.5 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626792 c.558G>T synonymous_variant 0.5 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626795 c.-182C>T upstream_gene_variant 0.5 bedaquiline
rifampicin
mtrB 3626798 c.-185T>C upstream_gene_variant 0.5 bedaquiline
rifampicin
mtrA 3626804 c.546A>G synonymous_variant 0.5 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626903 c.-290T>C upstream_gene_variant 0.38 bedaquiline
rifampicin
mtrB 3627065 c.-452G>C upstream_gene_variant 0.47 bedaquiline
rifampicin
mtrA 3627068 c.282T>C synonymous_variant 0.47 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627071 c.279G>T synonymous_variant 0.44 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627074 c.-461G>C upstream_gene_variant 0.44 bedaquiline
rifampicin
mtrA 3627080 c.270T>C synonymous_variant 0.44 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627083 c.-470G>C upstream_gene_variant 0.44 bedaquiline
rifampicin
mtrA 3627098 c.252A>C synonymous_variant 0.35 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627104 c.-491C>G upstream_gene_variant 0.37 bedaquiline
rifampicin
mtrA 3627119 c.231T>G synonymous_variant 0.33 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627122 c.-509T>C upstream_gene_variant 0.33 bedaquiline
rifampicin
rpoA 3877553 p.Glu319Gln missense_variant 0.67 rifampicin
rpoA 3877571 p.Pro313Ala missense_variant 0.67 rifampicin
rpoA 3877587 c.921A>G synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoA 3877613 p.Ile299Val missense_variant 0.55 rifampicin
rpoA 3877668 c.840A>G synonymous_variant 0.67 rifampicin
rpoA 3877679 p.Ala277Ser missense_variant 0.53 rifampicin
rpoA 3877686 c.822A>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoA 3877909 p.Asn200Ser missense_variant 0.46 rifampicin
rpoA 3877920 c.588G>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoA 3877923 c.585C>T synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoA 3877926 c.582G>C synonymous_variant 0.43 rifampicin
rpoA 3878199 c.309T>C synonymous_variant 0.41 rifampicin
rpoA 3878217 c.291A>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoA 3878226 c.282C>G synonymous_variant 0.38 rifampicin
rpoA 3878232 c.276G>C synonymous_variant 0.43 rifampicin
rpoA 3878247 c.261G>C synonymous_variant 0.45 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoA 3878284 p.Glu75Ala missense_variant 0.53 rifampicin
rpoA 3878292 c.216T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoA 3878424 c.84G>C synonymous_variant 0.47 rifampicin
rpoA 3878436 c.72A>G synonymous_variant 0.4 rifampicin
rpoA 3878442 c.66G>C synonymous_variant 0.39 rifampicin
rpoA 3878853 c.-346G>A upstream_gene_variant 0.33 rifampicin
rpoA 3879088 c.-581A>C upstream_gene_variant 0.3 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.3 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.79 pyrazinamide Not assoc w R
clpC1 4038640 p.Asp689Asn missense_variant 0.43 pyrazinamide
clpC1 4038653 c.2052C>T synonymous_variant 0.43 pyrazinamide
clpC1 4038658 p.Lys683Gln missense_variant 0.4 pyrazinamide
clpC1 4038661 p.Ser682Thr missense_variant 0.38 pyrazinamide
clpC1 4038662 c.2043T>C synonymous_variant 0.38 pyrazinamide
clpC1 4038671 c.2034T>C synonymous_variant 0.38 pyrazinamide
clpC1 4038755 c.1950G>T synonymous_variant 0.38 pyrazinamide
clpC1 4038770 c.1935C>T synonymous_variant 0.4 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.38 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.39 pyrazinamide
clpC1 4038812 c.1893T>C synonymous_variant 0.48 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.26 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.37 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.39 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.39 pyrazinamide Uncertain significance
clpC1 4039430 c.1275T>C synonymous_variant 0.44 pyrazinamide
clpC1 4039576 p.Ala377Pro missense_variant 0.46 pyrazinamide
clpC1 4039577 c.1128T>C synonymous_variant 0.46 pyrazinamide Not assoc w R - Interim
clpC1 4039589 c.1116G>C synonymous_variant 0.46 pyrazinamide
clpC1 4039610 c.1095G>C synonymous_variant 0.48 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.36 pyrazinamide
clpC1 4039661 c.1044T>G synonymous_variant 0.43 pyrazinamide
clpC1 4039664 c.1041G>C synonymous_variant 0.43 pyrazinamide
clpC1 4039790 c.915C>G synonymous_variant 0.44 pyrazinamide
clpC1 4039826 c.879C>G synonymous_variant 0.47 pyrazinamide
clpC1 4039831 c.874T>C synonymous_variant 0.44 pyrazinamide
clpC1 4039850 c.855T>C synonymous_variant 0.4 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.4 pyrazinamide
embC 4240726 c.864G>C synonymous_variant 0.57 ethambutol Not assoc w R - Interim
embC 4240780 c.918T>C synonymous_variant 0.4 ethambutol
embC 4240783 c.921G>C synonymous_variant 0.39 ethambutol
embA 4245083 c.1851A>C synonymous_variant 0.37 ethambutol
embA 4245089 c.1857G>C synonymous_variant 0.37 ethambutol
embA 4245101 c.1869G>C synonymous_variant 0.42 ethambutol
embA 4245137 c.1905T>C synonymous_variant 0.43 ethambutol
embB 4248130 c.1617G>C synonymous_variant 0.28 ethambutol
embB 4248142 c.1629T>C synonymous_variant 0.22 ethambutol
embB 4248143 c.1630T>C synonymous_variant 0.25 ethambutol
embB 4248157 c.1644A>G synonymous_variant 0.24 ethambutol Not assoc w R - Interim
embB 4248172 c.1659G>C synonymous_variant 0.29 ethambutol
embB 4248199 c.1686A>G synonymous_variant 0.33 ethambutol
embB 4248200 p.Ile563Val missense_variant 0.37 ethambutol
embB 4248205 c.1692C>G synonymous_variant 0.41 ethambutol
embB 4248206 c.1693_1695delAGCinsGT frameshift_variant&missense_variant 0.39 ethambutol
embB 4248220 c.1707A>C synonymous_variant 0.41 ethambutol
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 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R