TB-Profiler result

Run: SRR13861296
Summary

Run ID: SRR13861296

Sample name:

Date: 2025-09-15T16:23:10.933873

Number of reads: 2335408

Percentage reads mapped: 77.92

Median coverage: 79.0

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) None 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
dnaA 377 p.Thr126Asn missense_variant 1.0 isoniazid Uncertain significance
dnaA 1519 p.Arg507Ser missense_variant 1.0 isoniazid Uncertain significance
gyrB 5709 p.Gly157Val missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9028 p.Val576Ala missense_variant 0.94 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491212 p.Ser144Arg missense_variant 0.15 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fgd1 491217 c.435T>C synonymous_variant 0.14 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fgd1 491232 c.450T>C synonymous_variant 0.15 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fgd1 491241 p.Asp153Glu missense_variant 0.15 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fgd1 491244 c.462T>C synonymous_variant 0.13 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv0565c 657669 c.-199C>A upstream_gene_variant 0.97 ethionamide Uncertain significance
nusG 734472 c.219T>C synonymous_variant 0.13 rifampicin Uncertain significance
nusG 734475 c.222T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
nusG 734481 c.228C>G synonymous_variant 0.13 rifampicin Uncertain significance
nusG 734499 c.246G>C synonymous_variant 0.15 rifampicin Uncertain significance
nusG 734559 c.306T>C synonymous_variant 0.14 rifampicin Uncertain significance
nusG 734610 c.357C>G synonymous_variant 0.14 rifampicin Uncertain significance
mmaA3 737654 p.Ala166Ser missense_variant 1.0 isoniazid Uncertain significance
rpoB 762011 c.2205G>C synonymous_variant 0.91 rifampicin Not assoc w R - Interim
rpoB 762279 c.2474delA frameshift_variant 0.95 rifampicin Uncertain significance
rpoC 764752 c.1383G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.13 rifampicin Not assoc w R
rpoC 764824 c.1455T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764830 c.1461C>G synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 764858 c.1489T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoC 764911 c.1542A>G synonymous_variant 0.16 rifampicin Uncertain significance
rpoC 764923 c.1554A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764932 c.1563C>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 765007 c.1638T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
mmpS5 778823 p.Ile28Thr missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 800279 c.-530A>C upstream_gene_variant 1.0 linezolid Uncertain significance
fbiC 1304640 c.1710A>C synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv1258c 1406376 p.Gly322Val missense_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1853370 c.-236_-234delGCAinsTCG upstream_gene_variant 0.13 linezolid Uncertain significance
tsnR 1853384 c.-222G>C upstream_gene_variant 0.13 linezolid Uncertain significance
tsnR 1853394 c.-212_-211delCTinsGC upstream_gene_variant 0.14 linezolid Uncertain significance
tsnR 1853420 c.-186T>G upstream_gene_variant 0.14 linezolid Uncertain significance
tsnR 1853429 c.-177G>C upstream_gene_variant 0.13 linezolid Uncertain significance
tsnR 1853432 c.-174G>C upstream_gene_variant 0.13 linezolid Uncertain significance
PPE35 2169882 p.Ser244Ile missense_variant 1.0 pyrazinamide Uncertain significance
eis 2714940 c.392delA frameshift_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2477c 2782900 c.1143C>G synonymous_variant 0.99 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
ald 3087311 c.492C>G synonymous_variant 0.99 cycloserine Uncertain significance
Rv3236c 3613629 c.-513C>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
mtrB 3625750 c.864G>A synonymous_variant 0.13 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3625755 p.Ala287Thr missense_variant 0.13 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiB 3642465 p.Asp311His missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
alr 3840300 p.Pro350His missense_variant 0.99 cycloserine Uncertain significance
rpoA 3878288 p.Thr74Pro missense_variant 0.91 rifampicin Uncertain significance
clpC1 4038671 c.2034T>C synonymous_variant 0.12 pyrazinamide Uncertain significance
clpC1 4038740 c.1965G>C synonymous_variant 0.13 pyrazinamide Uncertain significance
clpC1 4038748 p.Arg653Cys missense_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039415 c.1289dupA frameshift_variant 0.96 pyrazinamide Uncertain significance
clpC1 4039524 p.Phe394Tyr missense_variant 0.12 pyrazinamide Uncertain significance
clpC1 4039576 p.Ala377Ser missense_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039577 c.1128T>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4039610 c.1095G>C synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039616 c.1089G>C synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4039622 c.1083C>G synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039685 c.1020C>T synonymous_variant 0.13 pyrazinamide Uncertain significance
clpC1 4040354 c.351A>G synonymous_variant 0.16 pyrazinamide Uncertain significance
clpC1 4040363 c.342A>C synonymous_variant 0.16 pyrazinamide Uncertain significance
clpC1 4040369 c.336C>G synonymous_variant 0.17 pyrazinamide Uncertain significance
clpC1 4040380 c.325T>C synonymous_variant 0.16 pyrazinamide Uncertain significance
clpC1 4040381 c.324T>C synonymous_variant 0.16 pyrazinamide Uncertain significance
clpC1 4040387 c.318A>G synonymous_variant 0.16 pyrazinamide Uncertain significance
clpC1 4040393 c.312G>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4040792 c.-88A>T upstream_gene_variant 1.0 pyrazinamide Uncertain significance
embA 4243235 c.3G>T synonymous_variant 1.0 ethambutol Uncertain significance