TB-Profiler result

Run: SRR28351224
Summary

Run ID: SRR28351224

Sample name:

Date: 2024-05-22T11:24:18.216046

Number of reads: 9065129

Percentage reads mapped: 99.75

Median coverage: 284.0

Strain: lineage2.2.1;lineage4.3.4.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.82
lineage2 East-Asian RD105 0.12
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.14
lineage2.2 East-Asian (Beijing) RD105;RD207 0.13
lineage4.3.4.1 Euro-American (LAM) RD174 0.86
lineage4 Euro-American None 0.87
lineage4.3.4 Euro-American (LAM) RD174 0.84
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
rpoC p.Ile491Thr Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-37G>T Assoc w R
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 0.19 rifampicin Assoc w R
rpoC 764841 p.Ile491Thr missense_variant 0.14 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.17 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.15 isoniazid Assoc w R High-level resistance
eis 2715369 c.-37G>T upstream_gene_variant 0.19 kanamycin 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
Rv0010c 13636 c.-78A>G upstream_gene_variant 0.15 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.2 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.16 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.13 rifampicin Not assoc w R
rpoC 763783 c.414G>A synonymous_variant 0.83 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.84 rifampicin Not assoc w R
rpoC 765325 c.1956C>T synonymous_variant 0.83 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.17 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.15 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 0.87 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
PPE35 2168147 c.2466A>G synonymous_variant 0.87 pyrazinamide Not assoc w R - Interim
PPE35 2169016 p.Thr533Ala missense_variant 0.17 pyrazinamide Uncertain significance
Rv1979c 2223123 c.42G>A synonymous_variant 0.76 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2746540 c.1059G>A synonymous_variant 0.84 para-aminosalicylic_acid
folC 2746747 c.852G>C synonymous_variant 0.17 para-aminosalicylic_acid
Rv2681 2996821 p.Gly28Ala missense_variant 0.85 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.84 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.81 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840710 c.711A>G synonymous_variant 0.92 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.86 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4327247 p.Ala76Asp missense_variant 0.16 ethionamide Uncertain significance
whiB6 4338550 c.-29A>T upstream_gene_variant 0.85 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
whiB6 4338735 c.-214C>G upstream_gene_variant 0.91 capreomycin
amikacin
kanamycin
gid 4407927 p.Glu92Asp missense_variant 0.16 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.87 streptomycin Not assoc w R