TB-Profiler result

Run: ERR1034816
Summary

Run ID: ERR1034816

Sample name:

Date: 2024-04-16T01:53:19.091151

Number of reads: 3499552

Percentage reads mapped: 99.71

Median coverage: 75.0

Strain: lineage4.3.4.2.1

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 1.0
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 1.0
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 1.0
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 katG c.267_268insT Assoc w R High-level resistance
c.267_268insT Assoc w R High-level resistance
ahpC c.-81C>T Uncertain significance Mutation from literature
c.-54C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Ser Assoc w R
pyrazinamide
streptomycin rpsL p.Lys88Gln Assoc w R - Interim
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
rpsL 781821 p.Lys88Gln missense_variant 0.43 streptomycin Assoc w R - Interim
katG 2155845 c.267_268insT frameshift_variant 0.65 isoniazid Assoc w R High-level resistance
katG 2155845 c.267_268insT frameshift_variant 0.65 isoniazid Assoc w R High-level resistance
ahpC 2726112 c.-81C>T upstream_gene_variant 0.41 isoniazid Uncertain significance Mutation from literature
ahpC 2726139 c.-54C>T upstream_gene_variant 0.17 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.42 ethambutol Assoc w R
embB 4247729 p.Gly406Ser missense_variant 0.45 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
gyrB 5936 p.Ala233Thr missense_variant 0.45 levofloxacin
moxifloxacin
gyrB 6140 p.Val301Leu missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
ndh 2103098 c.-56C>T upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
katG 2155845 c.267G>T synonymous_variant 0.31 isoniazid
katG 2155845 c.267G>T synonymous_variant 0.31 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243745 c.513C>A synonymous_variant 1.0 ethambutol
whiB6 4338455 c.65_66dupCA frameshift_variant 0.97 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338513 p.Tyr3* stop_gained 1.0 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
gid 4408006 p.Val66Glu missense_variant 0.39 streptomycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R