TB-Profiler result

Run: SRR13861296
Summary

Run ID: SRR13861296

Sample name:

Date: 2024-04-15T02:58:35.745696

Number of reads: 2335408

Percentage reads mapped: 77.92

Median coverage: 80.0

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 1.0
lineage4.9 Euro-American (H37Rv-like) 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
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
dnaA 1519 p.Arg507Ser missense_variant 1.0 isoniazid
gyrB 5709 p.Gly157Val missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9028 p.Val576Ala missense_variant 0.94 levofloxacin
moxifloxacin
fgd1 491212 p.Ser144Arg missense_variant 0.15 clofazimine
pretomanid
delamanid
fgd1 491217 c.435T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491232 c.450T>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fgd1 491241 p.Asp153Glu missense_variant 0.15 clofazimine
pretomanid
delamanid
fgd1 491244 c.462T>C synonymous_variant 0.13 clofazimine
pretomanid
delamanid
Rv0565c 657669 c.-199C>A upstream_gene_variant 0.97 ethionamide
nusG 734472 c.219T>C synonymous_variant 0.13 rifampicin
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
nusG 734499 c.246G>C synonymous_variant 0.15 rifampicin
nusG 734559 c.306T>C synonymous_variant 0.14 rifampicin
nusG 734610 c.357C>G synonymous_variant 0.14 rifampicin
rpoB 762011 c.2205G>C synonymous_variant 0.91 rifampicin Not assoc w R - Interim
rpoB 762279 c.2474delA frameshift_variant 0.95 rifampicin
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
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
rpoC 764911 c.1542A>G synonymous_variant 0.16 rifampicin
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 clofazimine
bedaquiline
rplC 800279 c.-530A>C upstream_gene_variant 1.0 linezolid
fbiC 1304640 c.1710A>C synonymous_variant 1.0 clofazimine
pretomanid
delamanid
Rv1258c 1406376 p.Gly322Val missense_variant 1.0 streptomycin
isoniazid
pyrazinamide
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
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
tsnR 1853370 c.-236_-234delGCAinsTG upstream_gene_variant 0.13 linezolid
tsnR 1853384 c.-222G>C upstream_gene_variant 0.13 linezolid
tsnR 1853394 c.-212_-211delCTinsGC upstream_gene_variant 0.14 linezolid
tsnR 1853420 c.-186T>G upstream_gene_variant 0.14 linezolid
tsnR 1853429 c.-177G>C upstream_gene_variant 0.13 linezolid
tsnR 1853432 c.-174G>C upstream_gene_variant 0.13 linezolid
PPE35 2169882 p.Ser244Ile missense_variant 1.0 pyrazinamide
eis 2714940 c.392delA frameshift_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2477c 2782900 c.1143C>G synonymous_variant 0.99 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3087311 c.492C>G synonymous_variant 0.99 cycloserine
Rv3236c 3613629 c.-513C>G upstream_gene_variant 1.0 pyrazinamide
mtrB 3625750 c.864G>A synonymous_variant 0.13 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625755 p.Ala287Thr missense_variant 0.13 bedaquiline
rifampicin Uncertain significance
fbiB 3642465 p.Asp311His missense_variant 1.0 clofazimine
pretomanid
delamanid
alr 3840300 p.Pro374His missense_variant 0.99 cycloserine
rpoA 3878288 p.Thr74Pro missense_variant 0.91 rifampicin
clpC1 4038671 c.2034T>C synonymous_variant 0.12 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038748 p.Arg653Cys missense_variant 0.14 pyrazinamide
clpC1 4039415 c.1289dupA frameshift_variant 0.96 pyrazinamide
clpC1 4039524 p.Phe394Tyr missense_variant 0.12 pyrazinamide
clpC1 4039576 p.Ala377Ser missense_variant 0.13 pyrazinamide
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
clpC1 4039616 c.1089G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039622 c.1083C>G synonymous_variant 0.14 pyrazinamide
clpC1 4039685 c.1020C>T synonymous_variant 0.13 pyrazinamide
clpC1 4040354 c.351A>G synonymous_variant 0.16 pyrazinamide
clpC1 4040363 c.342A>C synonymous_variant 0.16 pyrazinamide
clpC1 4040369 c.336C>G synonymous_variant 0.17 pyrazinamide
clpC1 4040380 c.325T>C synonymous_variant 0.16 pyrazinamide
clpC1 4040381 c.324T>C synonymous_variant 0.16 pyrazinamide
clpC1 4040387 c.318A>G synonymous_variant 0.16 pyrazinamide
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
embA 4243235 c.3G>T synonymous_variant 1.0 ethambutol