TB-Profiler result

Run: SRR26399255

Summary

Run ID: SRR26399255

Sample name:

Date: 16-03-2024 14:27:14

Number of reads: 525189

Percentage reads mapped: 94.03

Strain: lineage2.2.1

Drug-resistance: Sensitive


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.97
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.96
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760184 c.378A>G synonymous_variant 0.54
rpoB 760196 c.390C>G synonymous_variant 0.54
rpoB 761537 c.1731C>G synonymous_variant 0.39
rpoB 761573 c.1767C>G synonymous_variant 0.42
rpoB 761579 c.1773G>C synonymous_variant 0.4
rpoB 761606 c.1800C>G synonymous_variant 0.29
rpoB 762062 c.2256T>C synonymous_variant 0.53
rpoB 762065 c.2259T>C synonymous_variant 0.53
rpoB 762078 c.2272C>T synonymous_variant 0.59
rpoB 762083 c.2277T>C synonymous_variant 0.58
rpoB 762086 c.2280G>C synonymous_variant 0.58
rpoB 762101 c.2295C>G synonymous_variant 0.61
rpoB 762114 p.Ile770Val missense_variant 0.65
rpoB 762131 c.2325C>G synonymous_variant 0.67
rpoB 762134 c.2328C>G synonymous_variant 0.68
rpoB 762143 c.2337T>C synonymous_variant 0.67
rpoB 762149 c.2343G>C synonymous_variant 0.68
rpoB 762185 c.2379G>C synonymous_variant 0.66
rpoB 762221 c.2415G>A synonymous_variant 0.56
rpoB 762233 c.2427G>C synonymous_variant 0.52
rpoB 762254 c.2448T>C synonymous_variant 0.48
rpoB 762266 c.2460T>C synonymous_variant 0.45
rpoB 762284 c.2478G>C synonymous_variant 0.37
rpoB 762338 c.2532T>C synonymous_variant 0.45
rpoB 762347 c.2541T>C synonymous_variant 0.5
rpoB 762362 p.Glu852Asp missense_variant 0.52
rpoB 762368 c.2562G>A synonymous_variant 0.52
rpoB 762369 c.2563T>C synonymous_variant 0.52
rpoC 762374 c.-996G>C upstream_gene_variant 0.48
rpoC 762380 c.-990T>C upstream_gene_variant 0.5
rpoC 762395 c.-975G>C upstream_gene_variant 0.46
rpoC 762398 c.-972T>G upstream_gene_variant 0.48
rpoC 762401 c.-969G>C upstream_gene_variant 0.48
rpoC 762404 c.-966T>C upstream_gene_variant 0.48
rpoC 762407 c.-963G>C upstream_gene_variant 0.48
rpoC 762410 c.-960T>C upstream_gene_variant 0.48
rpoC 762416 c.-954A>G upstream_gene_variant 0.48
rpoC 762434 c.-936T>C upstream_gene_variant 0.48
rpoC 762449 c.-921C>A upstream_gene_variant 0.44
rpoC 762470 c.-900G>C upstream_gene_variant 0.46
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764551 c.1182G>C synonymous_variant 0.27
rpoC 764566 c.1197C>G synonymous_variant 0.27
rpoC 764575 c.1206T>G synonymous_variant 0.28
rpoC 764581 c.1212T>C synonymous_variant 0.28
rpoC 764593 c.1224C>T synonymous_variant 0.3
rpoC 764611 c.1242G>C synonymous_variant 0.3
rpoC 764632 c.1263T>C synonymous_variant 0.23
rpoC 766843 c.3474T>C synonymous_variant 0.5
rpoC 766861 c.3492G>C synonymous_variant 0.51
rpoC 766864 c.3495G>C synonymous_variant 0.52
rpoC 766894 c.3525T>C synonymous_variant 0.57
rpoC 766895 c.3526T>C synonymous_variant 0.57
rpoC 766900 c.3531T>C synonymous_variant 0.58
rpoC 766918 c.3549C>T synonymous_variant 0.63
rpoC 766933 c.3564A>G synonymous_variant 0.63
rpoC 766945 c.3576A>G synonymous_variant 0.64
rpoC 766963 c.3594T>C synonymous_variant 0.66
rpoC 766972 c.3603G>C synonymous_variant 0.67
rpoC 766996 c.3627C>T synonymous_variant 0.61
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.63
rpoC 767059 c.3690T>G synonymous_variant 0.58
rpoC 767062 c.3693C>A synonymous_variant 0.62
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.93
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rpsA 1833874 c.333T>C synonymous_variant 0.58
rpsA 1833894 p.Ala118Glu missense_variant 0.56
rpsA 1833928 c.387G>C synonymous_variant 0.45
rpsA 1833949 c.408T>C synonymous_variant 0.45
rpsA 1833979 c.438T>C synonymous_variant 0.44
rpsA 1833991 c.450C>T synonymous_variant 0.42
rpsA 1834000 c.459G>C synonymous_variant 0.5
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834186 c.645C>G synonymous_variant 0.35
rpsA 1834189 c.648G>C synonymous_variant 0.35
rpsA 1834477 c.936C>T synonymous_variant 0.6
rpsA 1834489 c.948T>C synonymous_variant 0.62
rpsA 1834498 c.957C>T synonymous_variant 0.6
rpsA 1834528 c.987T>C synonymous_variant 0.68
rpsA 1834546 c.1005T>C synonymous_variant 0.74
rpsA 1834600 c.1059G>C synonymous_variant 0.68
rpsA 1834606 c.1065C>T synonymous_variant 0.67
rpsA 1834609 c.1068T>C synonymous_variant 0.67
rpsA 1834633 c.1092A>G synonymous_variant 0.59
rpsA 1834639 c.1098T>C synonymous_variant 0.55
rpsA 1834654 p.Glu371Asp missense_variant 0.52
rpsA 1834669 c.1128G>C synonymous_variant 0.52
rpsA 1834690 c.1149T>C synonymous_variant 0.44
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4038860 c.1845G>A synonymous_variant 0.56
clpC1 4038878 c.1827A>G synonymous_variant 0.5
clpC1 4038881 c.1824C>T synonymous_variant 0.56
clpC1 4038890 c.1815G>A synonymous_variant 0.6
clpC1 4038905 c.1800A>C synonymous_variant 0.67
clpC1 4038908 c.1797C>G synonymous_variant 0.71
clpC1 4038911 c.1794G>T synonymous_variant 0.71
clpC1 4038914 c.1791G>C synonymous_variant 0.72
clpC1 4038917 c.1788C>T synonymous_variant 0.72
clpC1 4038923 c.1782A>G synonymous_variant 0.74
clpC1 4038932 c.1773G>A synonymous_variant 0.74
clpC1 4039022 c.1683A>G synonymous_variant 0.48
clpC1 4039064 c.1641C>T synonymous_variant 0.43
clpC1 4039073 c.1632C>G synonymous_variant 0.41
clpC1 4039079 c.1626C>G synonymous_variant 0.39
clpC1 4039082 c.1623C>T synonymous_variant 0.39
clpC1 4039085 c.1620A>G synonymous_variant 0.42
clpC1 4039097 c.1608G>T synonymous_variant 0.46
clpC1 4039106 c.1599G>C synonymous_variant 0.5
clpC1 4039112 c.1593C>G synonymous_variant 0.49
clpC1 4039556 c.1149G>C synonymous_variant 0.33
clpC1 4039559 c.1146C>G synonymous_variant 0.33
clpC1 4039570 c.1135delAinsCTC frameshift_variant&missense_variant 0.29
clpC1 4039575 c.1128_1129delTG frameshift_variant 0.31
clpC1 4039580 c.1125C>T synonymous_variant 0.3
clpC1 4039586 c.1119G>C synonymous_variant 0.3
clpC1 4039616 c.1089G>C synonymous_variant 0.27
clpC1 4039622 c.1083C>T synonymous_variant 0.29
clpC1 4039647 p.Glu353Ala missense_variant 0.21
clpC1 4040144 c.561G>C synonymous_variant 0.56
clpC1 4040147 c.558A>G synonymous_variant 0.56
clpC1 4040159 c.546G>C synonymous_variant 0.59
clpC1 4040162 c.543G>C synonymous_variant 0.59
clpC1 4040165 c.540G>C synonymous_variant 0.59
clpC1 4040168 c.537G>C synonymous_variant 0.54
clpC1 4040171 c.534C>G synonymous_variant 0.58
clpC1 4040200 c.505T>C synonymous_variant 0.52
clpC1 4040201 c.504C>G synonymous_variant 0.52
clpC1 4040204 c.501G>C synonymous_variant 0.52
clpC1 4040207 c.498T>C synonymous_variant 0.52
clpC1 4040213 c.490_492delTCTinsAGC synonymous_variant 0.5
clpC1 4040225 c.480A>C synonymous_variant 0.45
clpC1 4040228 c.477G>A synonymous_variant 0.47
clpC1 4040231 c.474C>G synonymous_variant 0.47
clpC1 4040237 c.468C>T synonymous_variant 0.45
clpC1 4040249 c.456A>G synonymous_variant 0.47
clpC1 4040258 c.447G>A synonymous_variant 0.47
clpC1 4040267 c.438A>G synonymous_variant 0.44
clpC1 4040277 c.427_428delTCinsAG synonymous_variant 0.34
clpC1 4040279 c.426C>G synonymous_variant 0.32
panD 4044150 c.132A>C synonymous_variant 0.38
panD 4044188 c.94T>C synonymous_variant 0.38
panD 4044195 c.87T>C synonymous_variant 0.4
panD 4044210 c.72C>A synonymous_variant 0.42
panD 4044231 p.Cys17Gln missense_variant 0.33
panD 4044237 c.45G>C synonymous_variant 0.32
panD 4044240 c.42G>C synonymous_variant 0.33
panD 4044261 c.21G>A synonymous_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0