TB-Profiler result

Run: SRR8651642
Summary

Run ID: SRR8651642

Sample name:

Date: 2025-08-03T06:46:54.297878

Number of reads: 1378373

Percentage reads mapped: 99.58

Median coverage: 61.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: Pre-XDR-TB

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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
lineage4.5 Euro-American RD122 100.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
isoniazid katG c.2044_2045insT Assoc w R High-level resistance
ahpC c.-81C>T Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Asp461His Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Asp461His Assoc w R - Interim
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1299dupG Assoc w R
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
gyrB 6620 p.Asp461His missense_variant 1.0 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
katG 2154067 c.2044_2045insT frameshift_variant 0.98 isoniazid Assoc w R High-level resistance
ahpC 2726112 c.-81C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
ethA 4326174 c.1299dupG frameshift_variant 1.0 ethionamide Assoc w R
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 7774 p.Gly158Val missense_variant 0.44 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7892 c.591G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13394 p.Trp55* stop_gained 1.0 isoniazid Uncertain significance
mshA 575726 p.Thr127Pro missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575729 p.Gln128Met missense_variant 0.98 ethionamide Uncertain significance
isoniazid Uncertain significance
ccsA 620029 c.139C>T synonymous_variant 1.0 amikacin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rpoC 764452 c.1083T>C synonymous_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776157 p.Asp775Gly missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253846 p.Ala230Asp missense_variant 0.95 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
embR 1416613 c.734dupC frameshift_variant 0.96 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
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
tlyA 1918226 p.Phe96Ser missense_variant 1.0 capreomycin Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2221919 p.Val416Met missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2288925 p.Phe106Cys missense_variant 1.0 pyrazinamide Uncertain significance
lpqB 3624893 c.18G>A synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640255 c.-288_-287insA upstream_gene_variant 0.85 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoA 3879070 c.-563G>A upstream_gene_variant 1.0 rifampicin Uncertain significance
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246163 c.-351G>A upstream_gene_variant 1.0 ethambutol Uncertain significance
embB 4247723 p.Pro404Thr missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269671 p.Val55Leu missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338421 c.100delT frameshift_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
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
gid 4408217 c.-15C>T upstream_gene_variant 1.0 streptomycin Uncertain significance