TB-Profiler result

Run: SRR22251329
Summary

Run ID: SRR22251329

Sample name:

Date: 2024-04-15T20:40:12.839162

Number of reads: 2156394

Percentage reads mapped: 97.72

Median coverage: 65.0

Strain: lineage2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.1 East-Asian (non-Beijing) 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
isoniazid
ethambutol
pyrazinamide
streptomycin gid c.102delG 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
gid 4408100 c.102delG 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 7963 p.Gly221Glu missense_variant 0.15 levofloxacin
moxifloxacin
gyrA 7970 c.669T>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
fgd1 491232 c.450T>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fgd1 491259 c.477T>C synonymous_variant 0.22 clofazimine
pretomanid
delamanid
fgd1 491268 c.486C>T synonymous_variant 0.19 clofazimine
pretomanid
delamanid
fgd1 491286 c.504G>C synonymous_variant 0.15 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 760718 c.912C>T synonymous_variant 0.17 rifampicin
rpoB 760724 c.918T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762813 p.Met1003Val missense_variant 0.15 rifampicin
rpoB 762818 c.3012C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762857 c.3051C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763900 c.531G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.23 rifampicin Not assoc w R
rpoC 764812 c.1443C>G synonymous_variant 0.23 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764833 c.1464A>G synonymous_variant 0.19 rifampicin
rpoC 764836 c.1467G>A synonymous_variant 0.19 rifampicin
rpoC 764842 c.1473C>T synonymous_variant 0.2 rifampicin
rpoC 764869 c.1500C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765121 c.1752G>A synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.24 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.22 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.14 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 778706 p.Val67Gly missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781832 c.273T>C synonymous_variant 0.16 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.16 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.19 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.17 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.18 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.17 streptomycin
rpsL 781904 c.345C>T synonymous_variant 0.17 streptomycin Not assoc w R - Interim
rpsL 781907 c.348T>C synonymous_variant 0.17 streptomycin
rpsL 781916 c.357T>G synonymous_variant 0.18 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.21 streptomycin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1304443 p.Ala505Thr missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
embR 1417272 p.Thr26Pro missense_variant 1.0 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833802 c.261A>G synonymous_variant 0.17 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.17 pyrazinamide
rpsA 1833817 c.276C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833820 c.279G>A synonymous_variant 0.17 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.17 pyrazinamide
rpsA 1833859 c.318C>T synonymous_variant 0.17 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.16 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.17 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834297 c.756C>G synonymous_variant 0.19 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.19 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1834369 c.828C>G synonymous_variant 0.18 pyrazinamide
rpsA 1834396 c.855G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.17 pyrazinamide
rpsA 1834459 c.918G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.16 pyrazinamide
rpsA 1834499 c.958C>T synonymous_variant 0.14 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
tlyA 1918306 p.Arg123Ser missense_variant 1.0 capreomycin
katG 2153961 c.2151G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518902 p.Ala263Val missense_variant 0.97 isoniazid
folC 2747026 c.573C>G synonymous_variant 0.16 para-aminosalicylic_acid
Rv2477c 2783374 c.669G>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783377 c.666C>G synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783395 c.648T>C synonymous_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783422 c.621T>G synonymous_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783427 p.Pro206Ala missense_variant 0.2 ethambutol Uncertain significance
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin Uncertain significance
amikacin
Rv2477c 2783428 c.615C>T synonymous_variant 0.2 ethambutol
moxifloxacin Not assoc w R - Interim
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 2783440 c.603T>C synonymous_variant 0.22 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783461 c.582T>C synonymous_variant 0.24 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783467 c.576G>C synonymous_variant 0.23 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783473 c.570A>G synonymous_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783499 c.544T>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783502 c.541T>C synonymous_variant 0.17 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 Not assoc w R - Interim
Rv2477c 2783512 c.531A>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783605 c.438T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783659 p.Glu128Asp missense_variant 0.2 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2477c 2783665 c.378A>G synonymous_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783790 p.Val85Ile missense_variant 0.89 ethambutol Not assoc w R
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625537 c.-627T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
lpqB 3625579 c.-669A>C upstream_gene_variant 0.16 bedaquiline
rifampicin
lpqB 3625588 c.-678G>A upstream_gene_variant 0.16 bedaquiline
rifampicin
lpqB 3625612 c.-702G>C upstream_gene_variant 0.19 bedaquiline
rifampicin
mtrB 3625623 p.Thr331Ala missense_variant 0.17 bedaquiline
rifampicin
lpqB 3625627 c.-717C>T upstream_gene_variant 0.18 bedaquiline
rifampicin
lpqB 3625630 c.-720C>G upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrB 3625638 p.Ala326Ser missense_variant 0.17 bedaquiline
rifampicin
lpqB 3625648 c.-738T>C upstream_gene_variant 0.19 bedaquiline
rifampicin
mtrB 3625656 c.958T>C synonymous_variant 0.21 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3625663 c.-753G>C upstream_gene_variant 0.22 bedaquiline
rifampicin
lpqB 3625675 c.-765G>C upstream_gene_variant 0.21 bedaquiline
rifampicin
lpqB 3625690 c.-780T>C upstream_gene_variant 0.2 bedaquiline
rifampicin
lpqB 3625696 c.-786A>G upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrB 3625699 c.915C>T synonymous_variant 0.2 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625720 c.894G>C synonymous_variant 0.22 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625723 c.-813C>T upstream_gene_variant 0.23 bedaquiline
rifampicin
lpqB 3625731 c.-821C>T upstream_gene_variant 0.24 bedaquiline
rifampicin
mtrB 3625744 c.870G>A synonymous_variant 0.26 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625747 c.867G>C synonymous_variant 0.26 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625753 c.859_861delGCCinsAT frameshift_variant&missense_variant 0.25 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625765 c.849C>G synonymous_variant 0.24 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625774 c.840G>A synonymous_variant 0.27 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625806 c.808A>C synonymous_variant 0.24 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625807 c.807C>G synonymous_variant 0.23 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625828 c.-918G>C upstream_gene_variant 0.23 bedaquiline
rifampicin
mtrB 3625852 c.762A>G synonymous_variant 0.22 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625867 c.747A>G synonymous_variant 0.2 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625912 c.702G>C synonymous_variant 0.21 bedaquiline
rifampicin
mtrB 3625915 c.699G>T synonymous_variant 0.2 bedaquiline
rifampicin
mtrB 3625927 c.687T>C synonymous_variant 0.2 bedaquiline
rifampicin
mtrB 3625936 c.678C>G synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625942 c.672C>T synonymous_variant 0.16 bedaquiline
rifampicin
mtrB 3625945 c.669A>G synonymous_variant 0.15 bedaquiline
rifampicin
mtrB 3625950 c.664C>T synonymous_variant 0.15 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625951 c.663A>G synonymous_variant 0.16 bedaquiline
rifampicin
mtrB 3625977 p.Gly213Ser missense_variant 0.15 bedaquiline
rifampicin
mtrB 3625978 c.636T>C synonymous_variant 0.15 bedaquiline
rifampicin
mtrB 3625987 c.627G>T synonymous_variant 0.16 bedaquiline
rifampicin
mtrB 3626029 c.585A>G synonymous_variant 0.17 bedaquiline
rifampicin
mtrB 3626035 c.579G>C synonymous_variant 0.17 bedaquiline
rifampicin
mtrB 3626705 c.-92G>T upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626711 c.-98T>C upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrA 3626741 c.609C>G synonymous_variant 0.17 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626744 c.-131G>C upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrB 3626750 c.-137T>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrA 3626759 c.591T>C synonymous_variant 0.21 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626774 c.574_576delAGGinsCC frameshift_variant&missense_variant 0.22 bedaquiline
rifampicin
mtrB 3626780 c.-167T>C upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrB 3626783 c.-170C>G upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrA 3626786 c.564A>G synonymous_variant 0.23 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626798 c.-185T>A upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrB 3626804 c.-191A>C upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrA 3626846 c.504G>A synonymous_variant 0.21 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626849 c.-236C>G upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrB 3626858 c.-245A>G upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626866 c.-253T>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626876 c.-263A>G upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626885 c.-272A>G upstream_gene_variant 0.2 bedaquiline
rifampicin
mtrB 3626890 c.-277T>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626891 c.-278G>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626903 c.-290T>A upstream_gene_variant 0.19 bedaquiline
rifampicin
mtrA 3626912 c.438T>C synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626930 c.-317A>G upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrA 3626939 p.Glu137Asp missense_variant 0.21 bedaquiline
rifampicin
mtrB 3626942 c.-329A>C upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrB 3626969 c.-356C>G upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626972 c.-359A>G upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626987 c.-374C>G upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrB 3626992 c.-379C>T upstream_gene_variant 0.2 bedaquiline
rifampicin
mtrB 3627011 c.-398T>C upstream_gene_variant 0.2 bedaquiline
rifampicin
mtrA 3627026 c.324G>A synonymous_variant 0.18 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3627059 c.-446G>C upstream_gene_variant 0.19 bedaquiline
rifampicin
mtrA 3627068 c.282T>C synonymous_variant 0.17 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627071 c.-458G>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrA 3627080 c.270T>C synonymous_variant 0.17 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627083 c.-470G>C upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrA 3627098 c.252A>C synonymous_variant 0.2 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627104 c.-491C>G upstream_gene_variant 0.2 bedaquiline
rifampicin
mtrB 3627110 c.-497G>C upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrA 3627119 c.231T>G synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627122 c.-509T>C upstream_gene_variant 0.16 bedaquiline
rifampicin
fbiA 3641110 p.Ala190Thr missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rpoA 3878974 c.-467C>G upstream_gene_variant 0.15 rifampicin
clpC1 4040841 c.-138delG upstream_gene_variant 1.0 pyrazinamide
embC 4240418 p.Gly186Cys missense_variant 0.98 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246088 c.2856A>G synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.22 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
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 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R