TB-Profiler result

Run: ERR176675
Summary

Run ID: ERR176675

Sample name:

Date: 2025-09-15T14:01:14.575996

Number of reads: 2934919

Percentage reads mapped: 88.89

Median coverage: 61.0

Strain: lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 100.0
lineage4.3 Euro-American (LAM) None 100.0
lineage4.3.4 Euro-American (LAM) RD174 100.0
lineage4.3.4.2 Euro-American (LAM) RD174 100.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 100.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrB 6140 p.Val301Leu missense_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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
ccsA 620748 c.858T>C synonymous_variant 0.13 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
ccsA 620778 c.888T>C synonymous_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
ccsA 620781 c.891C>G synonymous_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
ccsA 620783 p.Ala298Val missense_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
ccsA 620787 c.897C>A synonymous_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
ccsA 620796 c.906C>G synonymous_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 1.0 rifampicin Not assoc w R
nusG 734532 c.279A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
nusG 734541 c.288A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
nusG 734559 c.306T>C synonymous_variant 0.13 rifampicin Uncertain significance
nusG 734841 c.588G>T synonymous_variant 0.15 rifampicin Uncertain significance
nusG 734853 c.600A>G synonymous_variant 0.16 rifampicin Uncertain significance
nusG 734854 c.601T>C synonymous_variant 0.16 rifampicin Uncertain significance
nusG 734870 p.Ser206Asn missense_variant 0.17 rifampicin Uncertain significance
nusG 734895 c.642A>G synonymous_variant 0.13 rifampicin Uncertain significance
nusG 734910 c.657C>G synonymous_variant 0.16 rifampicin Uncertain significance
nusG 734913 c.660C>G synonymous_variant 0.16 rifampicin Uncertain significance
rpoB 760646 c.840C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760649 c.843G>C synonymous_variant 0.13 rifampicin Uncertain significance
rpoB 760655 c.849A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760793 c.987A>G synonymous_variant 0.12 rifampicin Uncertain significance
rpoB 760820 c.1014T>C synonymous_variant 0.12 rifampicin Uncertain significance
rpoB 760826 c.1020C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760830 c.1024T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760973 c.1167G>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoB 760982 c.1176G>T synonymous_variant 0.14 rifampicin Uncertain significance
rpoB 760985 c.1179G>T synonymous_variant 0.14 rifampicin Uncertain significance
rpoB 760991 c.1185G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761006 c.1200C>T synonymous_variant 0.18 rifampicin Uncertain significance
rpoB 761015 c.1209G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.2 rifampicin Uncertain significance
rpoB 761027 c.1221A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761051 c.1245G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761060 c.1254C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761063 c.1257C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761096 c.1290G>C synonymous_variant 0.16 rifampicin Uncertain significance
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.14 rifampicin Uncertain significance
rpoB 761102 c.1296A>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoB 761189 c.1383T>G synonymous_variant 0.13 rifampicin Uncertain significance
rpoB 761240 c.1434C>T synonymous_variant 0.12 rifampicin Uncertain significance
rpoB 761435 c.1629T>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoB 761438 c.1632G>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoB 761465 c.1659G>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761471 c.1665C>T synonymous_variant 0.17 rifampicin Uncertain significance
rpoB 761477 c.1671C>T synonymous_variant 0.18 rifampicin Uncertain significance
rpoB 761492 c.1686G>C synonymous_variant 0.16 rifampicin Uncertain significance
rpoB 761495 c.1689G>A synonymous_variant 0.16 rifampicin Uncertain significance
rpoB 761504 c.1698C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761510 c.1704T>C synonymous_variant 0.18 rifampicin Uncertain significance
rpoB 761531 c.1725C>G synonymous_variant 0.13 rifampicin Uncertain significance
rpoB 762008 c.2202C>G synonymous_variant 0.16 rifampicin Uncertain significance
rpoB 762014 c.2208C>T synonymous_variant 0.18 rifampicin Uncertain significance
rpoB 762047 c.2241G>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762062 c.2256T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762284 c.2478G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762369 c.2563T>C synonymous_variant 0.12 rifampicin Uncertain significance
rpoC 763726 c.357C>T synonymous_variant 0.12 rifampicin Uncertain significance
rpoC 763732 c.363C>G synonymous_variant 0.12 rifampicin Uncertain significance
rpoC 763741 c.372C>T synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 763744 c.375G>C synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 763765 c.396T>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763771 c.402C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763780 c.411C>G synonymous_variant 0.11 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.96 rifampicin Not assoc w R
rpoC 765934 c.2565C>T synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766309 c.2940G>A synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 766315 c.2946C>G synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 766321 c.2952C>G synonymous_variant 0.12 rifampicin Uncertain significance
rpoC 766348 c.2979A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766369 c.3000C>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766456 c.3087C>G synonymous_variant 0.13 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1303674 c.744C>G synonymous_variant 0.12 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rpsA 1833613 c.72C>A synonymous_variant 0.16 pyrazinamide Uncertain significance
rpsA 1833619 c.78A>C synonymous_variant 0.16 pyrazinamide Uncertain significance
rpsA 1833661 c.120A>G synonymous_variant 0.15 pyrazinamide Uncertain significance
rpsA 1833724 c.183C>G synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1833727 c.186G>C synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1833859 c.318C>T synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1833874 c.333T>C synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1833895 c.354G>C synonymous_variant 0.15 pyrazinamide Uncertain significance
rpsA 1833928 c.387G>C synonymous_variant 0.12 pyrazinamide Uncertain significance
rpsA 1833949 c.408T>C synonymous_variant 0.12 pyrazinamide Uncertain significance
rpsA 1834249 c.708T>C synonymous_variant 0.18 pyrazinamide Uncertain significance
rpsA 1834261 c.720A>G synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.21 pyrazinamide Uncertain significance
rpsA 1834297 c.756C>T synonymous_variant 0.21 pyrazinamide Uncertain significance
rpsA 1834303 c.762T>G synonymous_variant 0.19 pyrazinamide Uncertain significance
rpsA 1834306 c.765T>C synonymous_variant 0.19 pyrazinamide Uncertain significance
rpsA 1834336 c.795C>G synonymous_variant 0.21 pyrazinamide Uncertain significance
rpsA 1834348 c.807T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
rpsA 1834423 c.882G>T synonymous_variant 0.16 pyrazinamide Uncertain significance
rpsA 1834451 c.910T>C synonymous_variant 0.15 pyrazinamide Uncertain significance
rpsA 1834456 c.915T>G synonymous_variant 0.16 pyrazinamide Uncertain significance
rpsA 1834465 c.924T>C synonymous_variant 0.15 pyrazinamide Uncertain significance
rpsA 1834468 c.927A>G synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834477 c.936C>T synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
rpsA 1834489 c.948T>C synonymous_variant 0.12 pyrazinamide Uncertain significance
rpsA 1834519 c.978G>C synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834546 c.1005T>C synonymous_variant 0.2 pyrazinamide Uncertain significance
rpsA 1834555 c.1014T>G synonymous_variant 0.19 pyrazinamide Uncertain significance
rpsA 1834603 c.1062G>A synonymous_variant 0.2 pyrazinamide Uncertain significance
rpsA 1834609 c.1068T>C synonymous_variant 0.21 pyrazinamide Uncertain significance
rpsA 1834612 c.1071G>A synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
rpsA 1834633 c.1092A>G synonymous_variant 0.16 pyrazinamide Uncertain significance
rpsA 1834639 c.1098T>C synonymous_variant 0.15 pyrazinamide Uncertain significance
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2783846 p.Thr66Asn missense_variant 0.12 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783857 c.186C>G synonymous_variant 0.14 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783860 c.183T>C synonymous_variant 0.14 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.95 para-aminosalicylic_acid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.630A>G synonymous_variant 1.0 cycloserine Uncertain significance
rpoA 3877900 p.Ser203Thr missense_variant 0.12 rifampicin Uncertain significance
rpoA 3877920 c.588G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3878061 c.447G>C synonymous_variant 0.13 rifampicin Uncertain significance
rpoA 3878067 c.441C>G synonymous_variant 0.12 rifampicin Uncertain significance
rpoA 3878070 c.438T>C synonymous_variant 0.12 rifampicin Uncertain significance
rpoA 3878094 c.414C>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoA 3878415 c.93C>T synonymous_variant 0.14 rifampicin Uncertain significance
rpoA 3878418 c.90C>T synonymous_variant 0.14 rifampicin Uncertain significance
rpoA 3879049 c.-542A>G upstream_gene_variant 0.15 rifampicin Uncertain significance
rpoA 3879079 c.-572A>G upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoA 3879088 c.-581A>C upstream_gene_variant 0.2 rifampicin Uncertain significance
rpoA 3879094 c.-587T>C upstream_gene_variant 0.2 rifampicin Uncertain significance
rpoA 3879117 c.-610C>T upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoA 3879121 c.-614T>G upstream_gene_variant 0.18 rifampicin Uncertain significance
rpoA 3879127 c.-620T>C upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoA 3879178 c.-671T>G upstream_gene_variant 0.12 rifampicin Uncertain significance
ddn 3986630 c.-214C>G upstream_gene_variant 0.18 delamanid Uncertain significance
pretomanid Uncertain significance
ddn 3986636 c.-208C>G upstream_gene_variant 0.17 delamanid Uncertain significance
pretomanid Uncertain significance
ddn 3986648 c.-196C>G upstream_gene_variant 0.15 delamanid Uncertain significance
pretomanid Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038425 c.2280C>A synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4038444 p.Ala754Lys missense_variant 0.18 pyrazinamide Uncertain significance
clpC1 4038446 c.2259T>C synonymous_variant 0.19 pyrazinamide Uncertain significance
clpC1 4038456 p.Val750Glu missense_variant 0.23 pyrazinamide Uncertain significance
clpC1 4038486 p.Gly740Asn missense_variant 0.19 pyrazinamide Uncertain significance
clpC1 4038491 c.2214C>T synonymous_variant 0.19 pyrazinamide Uncertain significance
clpC1 4038502 p.Ile735Val missense_variant 0.24 pyrazinamide Uncertain significance
clpC1 4038508 c.2197C>T synonymous_variant 0.25 pyrazinamide Uncertain significance
clpC1 4038518 c.2187G>T synonymous_variant 0.22 pyrazinamide Uncertain significance
clpC1 4038530 p.Glu725Asp missense_variant 0.19 pyrazinamide Uncertain significance
clpC1 4038537 p.Thr723Ser missense_variant 0.18 pyrazinamide Uncertain significance
clpC1 4038539 c.2166G>C synonymous_variant 0.18 pyrazinamide Uncertain significance
clpC1 4038965 c.1740T>C synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4038971 c.1734T>C synonymous_variant 0.16 pyrazinamide Uncertain significance
clpC1 4038974 c.1731T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038989 c.1716T>C synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4038997 c.1708T>C synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
clpC1 4039004 c.1701C>G synonymous_variant 0.18 pyrazinamide Uncertain significance
clpC1 4039022 c.1683A>G synonymous_variant 0.2 pyrazinamide Uncertain significance
clpC1 4039025 c.1680C>G synonymous_variant 0.19 pyrazinamide Uncertain significance
clpC1 4039085 c.1620A>G synonymous_variant 0.16 pyrazinamide Uncertain significance
clpC1 4039097 c.1608G>C synonymous_variant 0.12 pyrazinamide Uncertain significance
clpC1 4039339 p.Thr456Pro missense_variant 0.12 pyrazinamide Uncertain significance
clpC1 4039361 c.1344C>A synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039430 c.1275T>C synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4039694 c.1011G>C synonymous_variant 0.13 pyrazinamide Uncertain significance
clpC1 4040021 c.684A>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4040024 c.681A>G synonymous_variant 0.12 pyrazinamide Uncertain significance
clpC1 4040033 c.672G>C synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4040057 c.648C>T synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4040309 c.396C>T synonymous_variant 0.13 pyrazinamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.99 streptomycin Not assoc w R