TB-Profiler result

Run: SRR6824364
Summary

Run ID: SRR6824364

Sample name:

Date: 2025-05-25T18:19:35.875987

Number of reads: 13009946

Percentage reads mapped: 99.64

Median coverage: 398.0

Strain: lineage2.2.1;lineage4

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
lineage2 East-Asian RD105 0.96
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.96
lineage2.2 East-Asian (Beijing) RD105;RD207 0.95
lineage4 Euro-American None 0.05
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Arg Assoc w R
isoniazid katG c.-11434_*169del Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA c.473delA Assoc w R
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.9 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761140 p.His445Arg missense_variant 0.95 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.95 streptomycin Assoc w R
katG 2153719 c.-11434_*169del transcript_ablation 0.95 isoniazid Assoc w R High-level resistance
pncA 2288768 c.473delA frameshift_variant 0.95 pyrazinamide Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.96 ethambutol 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.98 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
mshA 575907 p.Ala187Val missense_variant 0.94 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.92 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.96 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.95 ethionamide Uncertain significance
rpoB 760295 p.Asn163Lys missense_variant 0.95 rifampicin Uncertain significance
rpoB 762909 p.Ile1035Val missense_variant 0.94 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.94 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.93 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.93 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.95 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800657 c.-152G>T upstream_gene_variant 0.96 linezolid Uncertain significance
Rv1129c 1253454 p.Gly361Cys missense_variant 0.94 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.95 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.95 pyrazinamide Not assoc w R - Interim
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
PPE35 2167926 p.Leu896Ser missense_variant 0.96 pyrazinamide 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
ahpC 2726142 c.-51G>A upstream_gene_variant 0.93 isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3236c 3612601 non_coding_transcript_variant 0.92 pyrazinamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.95 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.97 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.96 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.93 ethambutol Not assoc w R
ethA 4326025 non_coding_transcript_variant 0.96 ethionamide 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 4407588 c.615A>G synonymous_variant 0.94 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.95 streptomycin Not assoc w R