TB-Profiler result

Run: ERR1034816
Summary

Run ID: ERR1034816

Sample name:

Date: 20-10-2023 23:19:02

Number of reads: 3499552

Percentage reads mapped: 99.71

Strain: lineage4.3.4.2.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R katG c.267_268insT (0.65), ahpC c.-81C>T (0.41), ahpC c.-54C>T (0.17)
Ethambutol R embB p.Met306Ile (0.42), embB p.Gly406Ser (0.45)
Pyrazinamide
Streptomycin R rpsL p.Lys88Gln (0.43)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 1.0
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781821 p.Lys88Gln missense_variant 0.43 streptomycin
katG 2155845 c.267_268insT frameshift_variant 0.65 isoniazid
ahpC 2726112 c.-81C>T upstream_gene_variant 0.41 isoniazid
ahpC 2726139 c.-54C>T upstream_gene_variant 0.17 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.42 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.45 ethambutol
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
gyrB 5936 p.Ala233Thr missense_variant 0.45
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103098 c.-56C>T upstream_gene_variant 1.0
katG 2155845 c.267G>T synonymous_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243745 c.513C>A synonymous_variant 1.0
whiB6 4338455 c.65_66dupCA frameshift_variant 0.97
whiB6 4338513 p.Tyr3* stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408006 p.Val66Glu missense_variant 0.39
gid 4408156 p.Leu16Arg missense_variant 1.0