TB-Profiler result

Run: SRR30049957
Summary

Run ID: SRR30049957

Sample name:

Date: 2025-02-11T14:49:12.276401

Number of reads: 2355628

Percentage reads mapped: 99.56

Median coverage: 112.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American 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
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 7766 c.465C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 1.0 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764716 c.1347G>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 764812 c.1443C>G synonymous_variant 0.1 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781276 c.-284A>C upstream_gene_variant 1.0 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833856 c.315A>G synonymous_variant 0.11 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.12 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.11 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.1 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.1 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.11 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.12 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.11 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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.24 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.19 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038596 c.2109A>G synonymous_variant 0.14 pyrazinamide
clpC1 4038623 c.2082A>G synonymous_variant 0.18 pyrazinamide
clpC1 4038640 p.Asp689Asn missense_variant 0.19 pyrazinamide
clpC1 4038653 c.2052C>T synonymous_variant 0.18 pyrazinamide
clpC1 4038658 p.Lys683Gln missense_variant 0.18 pyrazinamide
clpC1 4038661 p.Ser682Thr missense_variant 0.18 pyrazinamide
clpC1 4038662 c.2043T>C synonymous_variant 0.19 pyrazinamide
clpC1 4038671 c.2034T>C synonymous_variant 0.21 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 0.24 pyrazinamide
clpC1 4038701 c.2004G>C synonymous_variant 0.27 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 0.27 pyrazinamide
clpC1 4038707 c.1998C>G synonymous_variant 0.27 pyrazinamide
clpC1 4038710 c.1995G>C synonymous_variant 0.27 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.27 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 0.29 pyrazinamide
clpC1 4038755 c.1950G>C synonymous_variant 0.24 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.22 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.23 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.24 pyrazinamide
clpC1 4038815 c.1890G>T synonymous_variant 0.25 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.16 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.17 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.16 pyrazinamide
clpC1 4038932 c.1773G>C synonymous_variant 0.15 pyrazinamide
embC 4239298 c.-565C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4248390 p.Met626Thr missense_variant 1.0 ethambutol
aftB 4268234 c.603G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin