TB-Profiler result

Run: ERR2516745
Summary

Run ID: ERR2516745

Sample name:

Date: 2024-10-05T11:11:54.702175

Number of reads: 8394556

Percentage reads mapped: 99.67

Median coverage: 283.0

Strain: lineage3;lineage4.1

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 0.86
lineage4.1 Euro-American None 0.13
lineage4 Euro-American None 0.14
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
p.Ile480Thr Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoB 761245 p.Ile480Thr missense_variant 0.11 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.12 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4248003 p.Gln497Arg missense_variant 0.85 ethambutol 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
gyrA 9596 c.2295G>T synonymous_variant 0.88 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13277 c.282T>C synonymous_variant 0.91 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.93 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.83 ethionamide Not assoc w R - Interim
hadA 732110 p.Cys61Gly missense_variant 0.9 isoniazid Uncertain significance
nusG 734354 p.Pro34Leu missense_variant 0.88 rifampicin Not assoc w R
nusG 734753 p.Thr167Met missense_variant 0.92 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.89 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.89 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 764181 p.Asp271Gly missense_variant 0.88 rifampicin Not assoc w R
rpoC 764438 c.1069C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764724 p.Phe452Cys missense_variant 0.86 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.15 rifampicin Not assoc w R
rpoC 766789 c.3420G>A synonymous_variant 0.87 rifampicin Not assoc w R - Interim
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 0.87 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 0.11 linezolid
rplC 801019 p.Thr71Ala missense_variant 0.13 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.88 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406260 p.Pro361Ser missense_variant 0.84 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid 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
katG 2154724 p.Arg463Leu missense_variant 0.89 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.88 pyrazinamide Not assoc w R
PPE35 2170769 c.-157C>T upstream_gene_variant 0.88 pyrazinamide
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 0.89 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.85 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.87 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.88 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 3064837 p.Leu452Ser missense_variant 0.88 levofloxacin Uncertain significance
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3064857 c.1334delG frameshift_variant 0.87 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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
mtrA 3627390 c.-41G>A upstream_gene_variant 0.15 rifampicin Uncertain significance
bedaquiline
panD 4044872 c.-591C>T upstream_gene_variant 0.87 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.87 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 0.87 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 0.11 ethambutol Not assoc w R
embB 4247296 c.783G>A synonymous_variant 0.14 ethambutol Not assoc w R - Interim
embB 4249408 c.2895G>A synonymous_variant 0.16 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 0.91 streptomycin Not assoc w R