TB-Profiler result

Run: SRR3105791
Summary

Run ID: SRR3105791

Sample name:

Date: 2024-10-04T20:58:57.292736

Number of reads: 2390824

Percentage reads mapped: 99.04

Median coverage: 43.0

Strain: lineage3

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
lineage3 East-African-Indian RD750 0.94
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
isoniazid inhA c.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA c.-145_*3412del Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
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 gyrB p.Thr500Asn Uncertain significance Mutation from literature
gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
ethA c.675dupC 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 6738 p.Thr500Asn missense_variant 0.93 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7570 p.Ala90Val missense_variant 1.0 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 761095 p.Leu430Pro missense_variant 0.94 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.83 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.87 isoniazid Assoc w R High-level resistance
pncA 2285268 c.-145_*3412del transcript_ablation 0.95 pyrazinamide Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.82 ethambutol Assoc w R
ethA 4326798 c.675dupC frameshift_variant 0.82 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
gyrB 5081 c.-159_-158insA upstream_gene_variant 0.92 levofloxacin
moxifloxacin
gyrB 6240 p.Asp334Gly missense_variant 0.88 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 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 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.88 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.92 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.94 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 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
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
tlyA 1918404 c.465G>A synonymous_variant 0.94 capreomycin Not assoc w R - Interim
katG 2154102 c.2010C>T synonymous_variant 0.9 isoniazid
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 2289622 c.-382delA upstream_gene_variant 0.96 pyrazinamide
ahpC 2726051 c.-142G>A upstream_gene_variant 0.17 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.9 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.83 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 3065163 c.1029C>G synonymous_variant 0.9 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568689 c.-10G>A upstream_gene_variant 0.96 kanamycin
amikacin
streptomycin
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841356 p.Ser22Leu missense_variant 0.91 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.93 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.77 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 4242075 p.Arg738Gln missense_variant 0.95 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 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407966 p.Leu79Phe missense_variant 0.81 streptomycin Uncertain significance