TB-Profiler result

Run: SRR1140681
Summary

Run ID: SRR1140681

Sample name:

Date: 2024-10-04T09:34:26.651400

Number of reads: 2656778

Percentage reads mapped: 99.65

Median coverage: 49.0

Strain: lineage3.1.2.1;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 0.64
lineage4.3 Euro-American (LAM) None 0.29
lineage3.1.2 East-African-Indian RD750 0.62
lineage4 Euro-American None 0.41
lineage4.3.4 Euro-American (LAM) RD174 0.38
lineage4.3.4.2 Euro-American (LAM) RD174 0.37
lineage3.1.2.1 East-African-Indian RD750 0.61
lineage3.1 East-African-Indian RD750 0.43
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Lys Assoc w R
p.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Gln10Arg Assoc w R
streptomycin gid c.545delG Assoc w R
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 761100 p.Gln432Lys missense_variant 0.65 rifampicin Assoc w R
rpoB 761110 p.Asp435Val missense_variant 0.35 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Arg missense_variant 0.41 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.59 ethambutol Assoc w R
gid 4407657 c.545delG frameshift_variant 0.58 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 0.59 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.74 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.78 rifampicin Not assoc w R
rpoB 762101 c.2295C>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.59 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.66 rifampicin Not assoc w R
rpoC 764916 p.Leu516Pro missense_variant 0.63 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 0.65 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 0.62 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 2154724 p.Arg463Leu missense_variant 0.51 isoniazid Not assoc w R
katG 2154973 p.Thr380Ser missense_variant 0.28 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.7 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.66 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 0.54 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.49 pyrazinamide
eis 2714460 c.873G>A synonymous_variant 0.56 kanamycin
amikacin
ahpC 2726105 c.-88G>A upstream_gene_variant 0.52 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.53 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 3067141 c.-951delC upstream_gene_variant 0.55 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.31 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.46 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878878 c.-371T>C upstream_gene_variant 0.36 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.29 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.6 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.52 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 0.56 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4328019 c.-546G>A upstream_gene_variant 0.21 ethionamide
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 0.56 streptomycin Not assoc w R
gid 4407980 p.Pro75Ala missense_variant 0.43 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.25 streptomycin Not assoc w R