TB-Profiler result

Run: SRR25827477
Summary

Run ID: SRR25827477

Sample name:

Date: 2024-10-05T06:43:49.365058

Number of reads: 6955293

Percentage reads mapped: 98.77

Median coverage: 236.0

Strain: lineage3

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 0.82
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
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 0.2 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.12 isoniazid Assoc w R High-level resistance
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 5052 c.-188A>G upstream_gene_variant 0.82 levofloxacin
moxifloxacin
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 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 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.87 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.81 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.81 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.98 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 0.98 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
rpsL 781879 p.Val107Ala missense_variant 0.84 streptomycin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.13 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.98 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 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 0.81 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.83 pyrazinamide
eis 2714177 p.Leu386Ile missense_variant 0.13 kanamycin Uncertain significance
amikacin Uncertain significance
ahpC 2726105 c.-88G>A upstream_gene_variant 0.81 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.82 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
Rv2680 2996207 p.Ala35Thr missense_variant 0.75 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.14 ethionamide Uncertain significance
Rv3236c 3612563 p.Met185Thr missense_variant 0.81 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.16 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.82 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.76 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
embC 4241042 p.Asn394Asp missense_variant 0.14 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.76 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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 0.97 kanamycin
capreomycin
amikacin
whiB6 4338841 c.-320G>A upstream_gene_variant 0.81 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.99 streptomycin Not assoc w R