TB-Profiler result

Run: SRR29016869
Summary

Run ID: SRR29016869

Sample name:

Date: 2025-02-11T11:31:07.727580

Number of reads: 2881193

Percentage reads mapped: 99.43

Median coverage: 85.0

Strain: lineage3;lineage4.3.4.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.83
lineage4.3 Euro-American (LAM) None 0.19
lineage4 Euro-American None 0.19
lineage4.3.4 Euro-American (LAM) RD174 0.2
lineage4.3.4.2 Euro-American (LAM) RD174 0.21
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-11C>A Uncertain significance Mutation from literature
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
rpoB 761155 p.Ser450Leu missense_variant 0.91 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embA 4243222 c.-11C>A upstream_gene_variant 0.84 ethambutol Uncertain significance Mutation from literature
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 7968 p.Val223Ile missense_variant 0.86 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 0.83 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.78 ethionamide Not assoc w R - Interim
nusG 734129 c.-125G>T upstream_gene_variant 0.77 rifampicin Uncertain significance
mmaA3 738017 p.Glu45Lys missense_variant 0.19 isoniazid
rpoB 759746 c.-61C>T upstream_gene_variant 0.83 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.82 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.76 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 0.78 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1416522 p.Val276Met missense_variant 0.84 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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 0.86 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
pncA 2289047 c.195C>T synonymous_variant 0.86 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.89 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.79 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.89 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2752c 3065293 p.Val300Ala missense_variant 0.22 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.21 para-aminosalicylic_acid
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
alr 3841473 c.-53G>A upstream_gene_variant 0.82 cycloserine
rpoA 3878637 c.-130G>C upstream_gene_variant 0.24 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.19 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.82 pyrazinamide
glpK 4138462 c.1291_1293dupGGC conservative_inframe_insertion 0.21 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138554 p.Ile401Ser missense_variant 0.15 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138622 c.1134C>T synonymous_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4139650 p.Gly36Arg missense_variant 0.21 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4239763 c.-100C>T upstream_gene_variant 0.19 ethambutol Not assoc w R
embC 4241175 p.Ser438Phe missense_variant 0.81 ethambutol
embC 4242075 p.Arg738Gln missense_variant 0.8 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267714 p.Leu375Phe missense_variant 0.8 ethambutol
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
gid 4407588 c.615A>G synonymous_variant 0.89 streptomycin Not assoc w R
gid 4408126 p.Leu26Trp missense_variant 0.14 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.15 streptomycin Not assoc w R