TB-Profiler result

Run: SRR26399255
Summary

Run ID: SRR26399255

Sample name:

Date: 2024-03-27T00:20:31.647854

Number of reads: 525189

Percentage reads mapped: 94.03

Median coverage: 15.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.97
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.99
lineage2.2 East-Asian (Beijing) RD105;RD207 0.96
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
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
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
rpoB 760184 c.378A>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoB 761537 c.1731C>G synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 0.29 rifampicin
rpoB 762062 c.2256T>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoB 762078 c.2272C>T synonymous_variant 0.59 rifampicin
rpoB 762083 c.2277T>C synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.61 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.65 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.67 rifampicin
rpoB 762134 c.2328C>G synonymous_variant 0.68 rifampicin Not assoc w R - Interim
rpoB 762143 c.2337T>C synonymous_variant 0.67 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.68 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.66 rifampicin Not assoc w R - Interim
rpoB 762221 c.2415G>A synonymous_variant 0.56 rifampicin
rpoB 762233 c.2427G>C synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoB 762254 c.2448T>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoB 762266 c.2460T>C synonymous_variant 0.45 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 762338 c.2532T>C synonymous_variant 0.45 rifampicin
rpoB 762347 c.2541T>C synonymous_variant 0.5 rifampicin
rpoB 762362 p.Glu852Asp missense_variant 0.52 rifampicin
rpoB 762368 c.2562G>A synonymous_variant 0.52 rifampicin
rpoB 762369 c.2563T>C synonymous_variant 0.52 rifampicin
rpoC 762374 c.-996G>C upstream_gene_variant 0.48 rifampicin
rpoC 762380 c.-990T>C upstream_gene_variant 0.5 rifampicin
rpoC 762395 c.-975G>C upstream_gene_variant 0.46 rifampicin
rpoC 762398 c.-972T>G upstream_gene_variant 0.48 rifampicin
rpoC 762401 c.-969G>C upstream_gene_variant 0.48 rifampicin
rpoB 762404 c.2598T>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 762407 c.-963G>C upstream_gene_variant 0.48 rifampicin
rpoC 762410 c.-960T>C upstream_gene_variant 0.48 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 762434 c.-936T>C upstream_gene_variant 0.48 rifampicin
rpoB 762449 c.2643C>A synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 762470 c.2664G>C synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764551 c.1182G>C synonymous_variant 0.27 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.28 rifampicin
rpoC 764593 c.1224C>T synonymous_variant 0.3 rifampicin
rpoC 764611 c.1242G>C synonymous_variant 0.3 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 766843 c.3474T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>C synonymous_variant 0.51 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.52 rifampicin
rpoC 766894 c.3525T>C synonymous_variant 0.57 rifampicin
rpoC 766895 c.3526T>C synonymous_variant 0.57 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.58 rifampicin
rpoC 766918 c.3549C>T synonymous_variant 0.63 rifampicin Not assoc w R - Interim
rpoC 766933 c.3564A>G synonymous_variant 0.63 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.64 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.66 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.67 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.61 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.63 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.62 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.93 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rpsA 1833874 c.333T>C synonymous_variant 0.58 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.56 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.45 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.45 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.44 pyrazinamide
rpsA 1833991 c.450C>T synonymous_variant 0.42 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.5 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834186 c.645C>G synonymous_variant 0.35 pyrazinamide
rpsA 1834189 c.648G>C synonymous_variant 0.35 pyrazinamide
rpsA 1834477 c.936C>T synonymous_variant 0.6 pyrazinamide Not assoc w R - Interim
rpsA 1834489 c.948T>C synonymous_variant 0.62 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.6 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.68 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.74 pyrazinamide
rpsA 1834600 c.1059G>C synonymous_variant 0.68 pyrazinamide
rpsA 1834606 c.1065C>T synonymous_variant 0.67 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.67 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.59 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.55 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.52 pyrazinamide
rpsA 1834669 c.1128G>C synonymous_variant 0.52 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.44 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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626029 c.585A>G synonymous_variant 0.34 bedaquiline
rifampicin
mtrB 3626041 c.573C>G synonymous_variant 0.42 bedaquiline
rifampicin
mtrB 3626054 p.Leu187Ser missense_variant 0.41 bedaquiline
rifampicin
mtrB 3626062 c.552T>G synonymous_variant 0.38 bedaquiline
rifampicin
mtrB 3626070 p.Ile182Val missense_variant 0.38 bedaquiline
rifampicin
mtrB 3626077 c.537C>G synonymous_variant 0.38 bedaquiline
rifampicin
mtrB 3626083 c.531G>C synonymous_variant 0.39 bedaquiline
rifampicin
mtrB 3626092 c.522T>C synonymous_variant 0.35 bedaquiline
rifampicin
mtrB 3626095 p.Glu173Asp missense_variant 0.4 bedaquiline
rifampicin
mtrB 3626101 p.Gln171His missense_variant 0.41 bedaquiline
rifampicin
mtrB 3626110 c.504C>G synonymous_variant 0.38 bedaquiline
rifampicin
mtrB 3626131 c.483G>C synonymous_variant 0.31 bedaquiline
rifampicin
mtrB 3626137 c.477G>A synonymous_variant 0.35 bedaquiline
rifampicin
mtrB 3626562 p.Pro18Ser missense_variant 0.95 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3626723 c.627C>T synonymous_variant 0.32 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626750 c.-137T>C upstream_gene_variant 0.45 bedaquiline
rifampicin
mtrA 3626774 c.574_576delAGGinsCT frameshift_variant&missense_variant 0.52 bedaquiline
rifampicin
mtrB 3626780 c.-167T>C upstream_gene_variant 0.52 bedaquiline
rifampicin
mtrB 3626783 c.-170C>G upstream_gene_variant 0.52 bedaquiline
rifampicin
mtrA 3626786 c.564A>G synonymous_variant 0.52 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626804 c.-191A>C upstream_gene_variant 0.54 bedaquiline
rifampicin
mtrB 3626843 c.-230G>C upstream_gene_variant 0.7 bedaquiline
rifampicin
mtrA 3626846 c.504G>A synonymous_variant 0.7 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626849 c.-236C>T upstream_gene_variant 0.73 bedaquiline
rifampicin
mtrB 3626858 c.-245A>G upstream_gene_variant 0.75 bedaquiline
rifampicin
mtrB 3626866 c.-253T>C upstream_gene_variant 0.84 bedaquiline
rifampicin
mtrB 3626885 c.-272A>G upstream_gene_variant 0.76 bedaquiline
rifampicin
mtrB 3626890 c.-277T>C upstream_gene_variant 0.76 bedaquiline
rifampicin
mtrA 3626912 c.438T>C synonymous_variant 0.76 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626930 c.-317A>G upstream_gene_variant 0.76 bedaquiline
rifampicin
mtrA 3626939 p.Glu137Asp missense_variant 0.72 bedaquiline
rifampicin
mtrB 3626942 c.-329A>C upstream_gene_variant 0.75 bedaquiline
rifampicin
mtrB 3626969 c.-356C>G upstream_gene_variant 0.68 bedaquiline
rifampicin
mtrB 3626972 c.-359A>G upstream_gene_variant 0.68 bedaquiline
rifampicin
mtrB 3626993 c.-380G>C upstream_gene_variant 0.71 bedaquiline
rifampicin
mtrB 3627011 c.-398T>C upstream_gene_variant 0.66 bedaquiline
rifampicin
mtrB 3627017 c.-404G>A upstream_gene_variant 0.67 bedaquiline
rifampicin
clpC1 4038860 c.1845G>A synonymous_variant 0.56 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.5 pyrazinamide Not assoc w R - Interim
clpC1 4038881 c.1824C>T synonymous_variant 0.56 pyrazinamide
clpC1 4038890 c.1815G>A synonymous_variant 0.6 pyrazinamide
clpC1 4038905 c.1800A>C synonymous_variant 0.67 pyrazinamide
clpC1 4038908 c.1797C>G synonymous_variant 0.71 pyrazinamide
clpC1 4038911 c.1794G>T synonymous_variant 0.71 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.72 pyrazinamide
clpC1 4038917 c.1788C>T synonymous_variant 0.72 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.74 pyrazinamide
clpC1 4038932 c.1773G>A synonymous_variant 0.74 pyrazinamide Not assoc w R - Interim
clpC1 4039022 c.1683A>G synonymous_variant 0.48 pyrazinamide
clpC1 4039064 c.1641C>T synonymous_variant 0.43 pyrazinamide
clpC1 4039073 c.1632C>G synonymous_variant 0.41 pyrazinamide
clpC1 4039079 c.1626C>G synonymous_variant 0.39 pyrazinamide Not assoc w R - Interim
clpC1 4039082 c.1623C>T synonymous_variant 0.39 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.42 pyrazinamide
clpC1 4039097 c.1608G>T synonymous_variant 0.46 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.5 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.49 pyrazinamide
clpC1 4039556 c.1149G>C synonymous_variant 0.33 pyrazinamide
clpC1 4039559 c.1146C>G synonymous_variant 0.33 pyrazinamide
clpC1 4039570 c.1135delAinsCTC frameshift_variant&missense_variant 0.29 pyrazinamide
clpC1 4039575 c.1128_1129delTG frameshift_variant 0.31 pyrazinamide
clpC1 4039580 c.1125C>T synonymous_variant 0.3 pyrazinamide
clpC1 4039586 c.1119G>C synonymous_variant 0.3 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.27 pyrazinamide
clpC1 4039622 c.1083C>T synonymous_variant 0.29 pyrazinamide
clpC1 4039647 p.Glu353Ala missense_variant 0.21 pyrazinamide
clpC1 4040144 c.561G>C synonymous_variant 0.56 pyrazinamide
clpC1 4040147 c.558A>G synonymous_variant 0.56 pyrazinamide Not assoc w R - Interim
clpC1 4040159 c.546G>C synonymous_variant 0.59 pyrazinamide
clpC1 4040162 c.543G>C synonymous_variant 0.59 pyrazinamide Not assoc w R - Interim
clpC1 4040165 c.540G>C synonymous_variant 0.59 pyrazinamide
clpC1 4040168 c.537G>C synonymous_variant 0.54 pyrazinamide
clpC1 4040171 c.534C>G synonymous_variant 0.58 pyrazinamide
clpC1 4040200 c.505T>C synonymous_variant 0.52 pyrazinamide
clpC1 4040201 c.504C>G synonymous_variant 0.52 pyrazinamide
clpC1 4040204 c.501G>C synonymous_variant 0.52 pyrazinamide
clpC1 4040207 c.498T>C synonymous_variant 0.52 pyrazinamide
clpC1 4040213 c.490_492delTCTinsAGC synonymous_variant 0.5 pyrazinamide
clpC1 4040225 c.480A>C synonymous_variant 0.45 pyrazinamide
clpC1 4040228 c.477G>A synonymous_variant 0.47 pyrazinamide
clpC1 4040231 c.474C>G synonymous_variant 0.47 pyrazinamide
clpC1 4040237 c.468C>T synonymous_variant 0.45 pyrazinamide
clpC1 4040249 c.456A>G synonymous_variant 0.47 pyrazinamide
clpC1 4040258 c.447G>A synonymous_variant 0.47 pyrazinamide
clpC1 4040267 c.438A>G synonymous_variant 0.44 pyrazinamide Not assoc w R - Interim
clpC1 4040277 c.427_428delTCinsAG synonymous_variant 0.34 pyrazinamide
clpC1 4040279 c.426C>G synonymous_variant 0.32 pyrazinamide Not assoc w R - Interim
panD 4044150 c.132A>C synonymous_variant 0.38 pyrazinamide
panD 4044188 c.94T>C synonymous_variant 0.38 pyrazinamide
panD 4044195 c.87T>C synonymous_variant 0.4 pyrazinamide
panD 4044210 c.72C>A synonymous_variant 0.42 pyrazinamide
panD 4044231 p.Cys17Gln missense_variant 0.33 pyrazinamide
panD 4044237 c.45G>C synonymous_variant 0.32 pyrazinamide
panD 4044240 c.42G>C synonymous_variant 0.33 pyrazinamide
panD 4044261 c.21G>A synonymous_variant 0.35 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R