TB-Profiler result

Run: SRR5341398
Summary

Run ID: SRR5341398

Sample name:

Date: 2024-10-05T09:08:56.104169

Number of reads: 1715335

Percentage reads mapped: 99.51

Median coverage: 50.0

Strain: lineage3;lineage4.1.1.3

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 0.63
lineage4.1 Euro-American None 0.36
lineage4.1.1.3 Euro-American (X-type) RD193 0.33
lineage4 Euro-American None 0.31
lineage4.1.1 Euro-American (X-type) None 0.37
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. 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.Met306Ile Assoc w R
p.Tyr319Ser Assoc w R
pyrazinamide pncA c.382dupG Assoc w R
streptomycin gid p.Gln125* Assoc w R
c.79delG 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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 0.62 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.5 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288859 c.382dupG frameshift_variant 0.61 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.64 ethambutol Assoc w R
embB 4247469 p.Tyr319Ser missense_variant 0.33 ethambutol Assoc w R
gid 4407830 p.Gln125* stop_gained 0.33 streptomycin Assoc w R
gid 4408123 c.79delG frameshift_variant 0.56 streptomycin 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 0.55 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.57 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.32 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.6 rifampicin Not assoc w R
rpoB 761993 c.2187C>T synonymous_variant 0.7 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.57 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.84 rifampicin Not assoc w R
rpoC 764819 p.Trp484Gly missense_variant 0.67 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.39 rifampicin Not assoc w R
rpoC 766196 p.Asp943Asn missense_variant 0.34 rifampicin Uncertain significance
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 0.7 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
rplC 800219 c.-590T>C upstream_gene_variant 0.43 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.75 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
katG 2153915 p.Asn733Asp missense_variant 0.42 isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.75 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.57 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 0.58 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.73 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.61 isoniazid Not assoc w R
folC 2747466 c.130_132dupGAT conservative_inframe_insertion 0.76 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.71 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 3064991 p.Arg401Gly missense_variant 0.55 levofloxacin
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
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
mtrB 3626068 c.546C>T synonymous_variant 0.52 rifampicin
bedaquiline
alr 3841473 c.-53G>A upstream_gene_variant 0.69 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.72 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 0.66 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.41 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.33 ethambutol Not assoc w R
ubiA 4269320 p.Leu172Val missense_variant 0.39 ethambutol Uncertain significance
ethR 4327691 p.Asp48Gly missense_variant 0.43 ethionamide Uncertain significance
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 0.63 streptomycin Not assoc w R