TB-Profiler result

Run: ERR4812883
Summary

Run ID: ERR4812883

Sample name:

Date: 20-10-2023 05:01:38

Number of reads: 3172809

Percentage reads mapped: 99.81

Strain: lineage4.9

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 (0.84)
Isoniazid R katG p.Ser315Thr (0.80)
Ethambutol R embB p.Asp354Ala (0.82)
Pyrazinamide R pncA p.Thr135Pro (0.81)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine R mmpR5 c.198dupG (0.89)
Para-aminosalicylic_acid
Delamanid
Bedaquiline R mmpR5 c.198dupG (0.89)
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
lineage4.9 Euro-American (H37Rv-like) T1 None 0.17
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 0.84 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.89 clofazimine, bedaquiline
katG 2155168 p.Ser315Thr missense_variant 0.8 isoniazid
pncA 2288839 p.Thr135Pro missense_variant 0.81 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 0.82 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
gyrA 7362 p.Glu21Gln missense_variant 0.86
gyrA 7585 p.Ser95Thr missense_variant 0.88
gyrA 9304 p.Gly668Asp missense_variant 0.84
mshA 575837 c.490C>T synonymous_variant 0.91
rpoB 761889 p.Val695Leu missense_variant 0.83
rpoC 764666 p.Gly433Ser missense_variant 0.87
mmpL5 775639 p.Ile948Val missense_variant 0.81
mmpL5 777875 c.605delG frameshift_variant 0.91
rpsL 781395 c.-165T>C upstream_gene_variant 0.9
rplC 801009 c.201A>G synonymous_variant 0.82
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.92
ndh 2101831 c.1212G>A synonymous_variant 0.88
katG 2156173 c.-62C>A upstream_gene_variant 0.91
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.81
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.81
ahpC 2726141 c.-52C>A upstream_gene_variant 0.85
Rv2752c 3065517 c.675C>T synonymous_variant 0.84
thyA 3074495 c.-24C>T upstream_gene_variant 0.9
fprA 3474299 p.Asp98Gly missense_variant 0.92
Rv3236c 3612219 p.Val300Ile missense_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 0.81
ethA 4326458 p.Ile339Ser missense_variant 0.9
ethA 4328317 c.-844C>T upstream_gene_variant 0.86
whiB6 4338595 c.-75delG upstream_gene_variant 0.87
gid 4407967 p.Leu79Trp missense_variant 0.82