TB-Profiler result

Run: ERR176675
Summary

Run ID: ERR176675

Sample name:

Date: 2024-10-04T12:40:18.334374

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
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 1.0
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 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
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 kanamycin
capreomycin
amikacin
ccsA 620778 c.888T>C synonymous_variant 0.14 kanamycin
capreomycin
amikacin
ccsA 620781 c.891C>G synonymous_variant 0.14 kanamycin
capreomycin
amikacin
ccsA 620783 p.Ala298Val missense_variant 0.14 kanamycin
capreomycin
amikacin
ccsA 620787 c.897C>A synonymous_variant 0.14 kanamycin
capreomycin
amikacin
ccsA 620796 c.906C>G synonymous_variant 0.14 kanamycin
capreomycin
amikacin
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
nusG 734841 c.588G>T synonymous_variant 0.15 rifampicin
nusG 734853 c.600A>G synonymous_variant 0.16 rifampicin
nusG 734854 c.601T>C synonymous_variant 0.16 rifampicin
nusG 734870 p.Ser206Asn missense_variant 0.17 rifampicin
nusG 734895 c.642A>G synonymous_variant 0.13 rifampicin
nusG 734910 c.657C>G synonymous_variant 0.16 rifampicin
nusG 734913 c.660C>G synonymous_variant 0.16 rifampicin
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
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
rpoB 760820 c.1014T>C synonymous_variant 0.12 rifampicin
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
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 761006 c.1200C>T synonymous_variant 0.18 rifampicin
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
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
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.14 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.14 rifampicin
rpoB 761189 c.1383T>G synonymous_variant 0.13 rifampicin
rpoB 761240 c.1434C>T synonymous_variant 0.12 rifampicin
rpoB 761435 c.1629T>C synonymous_variant 0.15 rifampicin
rpoB 761438 c.1632G>C synonymous_variant 0.15 rifampicin
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
rpoB 761477 c.1671C>T synonymous_variant 0.18 rifampicin
rpoB 761492 c.1686G>C synonymous_variant 0.16 rifampicin
rpoB 761495 c.1689G>A synonymous_variant 0.16 rifampicin
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
rpoB 761531 c.1725C>G synonymous_variant 0.13 rifampicin
rpoB 762008 c.2202C>G synonymous_variant 0.16 rifampicin
rpoB 762014 c.2208C>T synonymous_variant 0.18 rifampicin
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
rpoC 763726 c.357C>T synonymous_variant 0.12 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.12 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.13 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.13 rifampicin
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
rpoC 764995 c.1626C>G synonymous_variant 0.96 rifampicin Not assoc w R
rpoC 765934 c.2565C>T synonymous_variant 0.14 rifampicin
rpoC 766309 c.2940G>A synonymous_variant 0.13 rifampicin
rpoC 766315 c.2946C>G synonymous_variant 0.13 rifampicin
rpoC 766321 c.2952C>G synonymous_variant 0.12 rifampicin
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
rpoC 766456 c.3087C>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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1303674 c.744C>G synonymous_variant 0.12 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833613 c.72C>A synonymous_variant 0.16 pyrazinamide
rpsA 1833619 c.78A>C synonymous_variant 0.16 pyrazinamide
rpsA 1833661 c.120A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833859 c.318C>T synonymous_variant 0.13 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833895 c.354G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.12 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.18 pyrazinamide
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
rpsA 1834297 c.756C>T synonymous_variant 0.21 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.19 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834336 c.795C>G synonymous_variant 0.21 pyrazinamide
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
rpsA 1834451 c.910T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.16 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.14 pyrazinamide
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
rpsA 1834519 c.978G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834555 c.1014T>G synonymous_variant 0.19 pyrazinamide
rpsA 1834603 c.1062G>A synonymous_variant 0.2 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.21 pyrazinamide
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
rpsA 1834639 c.1098T>C synonymous_variant 0.15 pyrazinamide
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 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783857 c.186C>G synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783860 c.183T>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyA 3073868 p.Thr202Ala missense_variant 0.95 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
rpoA 3877900 p.Ser203Thr missense_variant 0.12 rifampicin
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
rpoA 3878067 c.441C>G synonymous_variant 0.12 rifampicin
rpoA 3878070 c.438T>C synonymous_variant 0.12 rifampicin
rpoA 3878094 c.414C>G synonymous_variant 0.14 rifampicin
rpoA 3878415 c.93C>T synonymous_variant 0.14 rifampicin
rpoA 3878418 c.90C>T synonymous_variant 0.14 rifampicin
rpoA 3879049 c.-542A>G upstream_gene_variant 0.15 rifampicin
rpoA 3879079 c.-572A>G upstream_gene_variant 0.17 rifampicin
rpoA 3879088 c.-581A>C upstream_gene_variant 0.2 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.2 rifampicin
rpoA 3879117 c.-610C>T upstream_gene_variant 0.17 rifampicin
rpoA 3879121 c.-614T>G upstream_gene_variant 0.18 rifampicin
rpoA 3879127 c.-620T>C upstream_gene_variant 0.16 rifampicin
rpoA 3879178 c.-671T>G upstream_gene_variant 0.12 rifampicin
ddn 3986630 c.-214C>G upstream_gene_variant 0.18 pretomanid
delamanid
ddn 3986636 c.-208C>G upstream_gene_variant 0.17 pretomanid
delamanid
ddn 3986648 c.-196C>G upstream_gene_variant 0.15 pretomanid
delamanid
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038425 c.2280C>A synonymous_variant 0.15 pyrazinamide
clpC1 4038444 p.Ala754Lys missense_variant 0.18 pyrazinamide
clpC1 4038446 c.2259T>C synonymous_variant 0.19 pyrazinamide
clpC1 4038456 p.Val750Glu missense_variant 0.23 pyrazinamide
clpC1 4038486 p.Gly740Asn missense_variant 0.19 pyrazinamide
clpC1 4038491 c.2214C>T synonymous_variant 0.19 pyrazinamide
clpC1 4038502 p.Ile735Val missense_variant 0.24 pyrazinamide
clpC1 4038508 c.2197C>T synonymous_variant 0.25 pyrazinamide
clpC1 4038518 c.2187G>T synonymous_variant 0.22 pyrazinamide
clpC1 4038530 p.Glu725Asp missense_variant 0.19 pyrazinamide
clpC1 4038537 p.Thr723Ser missense_variant 0.18 pyrazinamide
clpC1 4038539 c.2166G>C synonymous_variant 0.18 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.16 pyrazinamide
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
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
clpC1 4039022 c.1683A>G synonymous_variant 0.2 pyrazinamide
clpC1 4039025 c.1680C>G synonymous_variant 0.19 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.16 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.12 pyrazinamide
clpC1 4039339 p.Thr456Pro missense_variant 0.12 pyrazinamide
clpC1 4039361 c.1344C>A synonymous_variant 0.14 pyrazinamide
clpC1 4039430 c.1275T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039694 c.1011G>C synonymous_variant 0.13 pyrazinamide
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
clpC1 4040033 c.672G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040057 c.648C>T synonymous_variant 0.14 pyrazinamide
clpC1 4040309 c.396C>T synonymous_variant 0.13 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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 4408156 p.Leu16Arg missense_variant 0.99 streptomycin Not assoc w R