TB-Profiler result

Run: SRR6982231
Summary

Run ID: SRR6982231

Sample name:

Date: 2025-07-28T12:24:08.466459

Number of reads: 2111957

Percentage reads mapped: 99.6

Median coverage: 109.0

Strain: lineage4.1.2;lineage4.2.2.2

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
lineage4.1 Euro-American None 76.79
lineage4.1.2 Euro-American None 75.43
lineage4.2 Euro-American None 23.87
lineage4.2.2 Euro-American (Ural) None 26.45
lineage4.2.2.2 Euro-American (Ural) None 21.46
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
gyrB 5077 c.-163_-162insC upstream_gene_variant 0.72 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8688 p.Ala463Ser missense_variant 0.17 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
mshA 576077 c.730C>T synonymous_variant 0.27 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.67 ethionamide Uncertain significance
Rv0565c 657425 p.Gly16Ser missense_variant 0.24 ethionamide Uncertain significance
rpoB 761489 c.1683G>A synonymous_variant 0.33 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.74 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 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.23 linezolid Uncertain significance
embR 1417140 p.Ala70Ser missense_variant 0.7 ethambutol Not assoc w R
embR 1418018 c.-671C>T upstream_gene_variant 0.72 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
inhA 1673249 c.-953C>T upstream_gene_variant 0.75 ethionamide Uncertain significance
isoniazid Uncertain significance
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
bacA 2063685 c.1044G>A synonymous_variant 0.19 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
bacA 2063911 p.Ile273Thr missense_variant 0.19 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
PPE35 2168990 c.1545_1622delGGCGATGACGCCAGCTAACATCACGGTGGGTGCGTTTGATTTGCCGGGGTTGACGGTGCCGTCGTTGACGATTCCAGC disruptive_inframe_deletion 1.0 pyrazinamide Uncertain significance
PPE35 2168990 p.AlaMetThrProAlaAsnIle516ValThrThrProAlaAsnVal missense_variant 0.36 pyrazinamide Uncertain significance
PPE35 2168990 c.1545_1622delGGCGATGACGCCAGCTAACATCACGGTGGGTGCGTTTGATTTGCCGGGGTTGACGGTGCCGTCGTTGACGATTCCAGC disruptive_inframe_deletion 0.64 pyrazinamide Uncertain significance
PPE35 2169071 c.1542A>G synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223658 c.-494C>G upstream_gene_variant 0.78 bedaquiline Uncertain significance
clofazimine Uncertain significance
folC 2747022 p.Val193Ile missense_variant 0.82 para-aminosalicylic_acid Uncertain significance
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.18 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
ald 3086742 c.-78A>C upstream_gene_variant 0.21 cycloserine Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine Uncertain significance
Rv3083 3448894 p.Tyr131Asp missense_variant 0.82 ethionamide Uncertain significance
Rv3083 3449642 p.Asn380Ser missense_variant 0.87 ethionamide Uncertain significance
whiB7 3568921 c.-242G>C upstream_gene_variant 0.78 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.95 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641164 p.Ile208Val missense_variant 0.87 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.67 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance