TB-Profiler result

Run: ERR038741

Summary

Run ID: ERR038741

Sample name:

Date: 20-10-2023 23:43:02

Number of reads: 10835450

Percentage reads mapped: 99.41

Strain: lineage4.2.2.2

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.His445Asp (0.99)
Isoniazid R ahpC c.-81C>T (1.00)
Ethambutol R embA c.-16C>T (1.00), embB p.Asp354Ala (0.99)
Pyrazinamide R pncA c.459_462dupCAGG (0.99)
Streptomycin
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 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 761139 p.His445Asp missense_variant 0.99 rifampicin
pncA 2288779 c.459_462dupCAGG frameshift_variant 0.99 pyrazinamide
ahpC 2726112 c.-81C>T upstream_gene_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247574 p.Asp354Ala missense_variant 0.99 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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoC 764613 p.Gln415Arg missense_variant 1.0
rpoC 766163 p.Glu932Lys missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474900 n.1243G>T non_coding_transcript_exon_variant 0.97
rpsA 1834013 p.Val158Leu missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154224 p.Gly630Arg missense_variant 1.0
PPE35 2169044 c.1569G>C synonymous_variant 1.0
Rv1979c 2221919 p.Val416Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714929 p.Thr135Ser missense_variant 1.0
eis 2715270 c.63G>C synonymous_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408072 p.Leu44Arg missense_variant 0.99