TB-Profiler result

Run: ERR4829975
Summary

Run ID: ERR4829975

Sample name:

Date: 20-10-2023 07:12:49

Number of reads: 3634922

Percentage reads mapped: 99.6

Strain: lineage4.9;lineage4.5

Drug-resistance: Pre-XDR-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 (0.25)
Isoniazid
Ethambutol R embB p.Met306Val (0.16)
Pyrazinamide R pncA p.Pro54Leu (0.15)
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (0.16)
Moxifloxacin R gyrA p.Ala90Val (0.16)
Ofloxacin R gyrA p.Ala90Val (0.16)
Levofloxacin R gyrA p.Ala90Val (0.16)
Ciprofloxacin R gyrA p.Ala90Val (0.16)
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
lineage4.5 Euro-American H;T RD122 0.88
lineage4.9 Euro-American (H37Rv-like) T1 None 0.13
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
gyrA 7570 p.Ala90Val missense_variant 0.16 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.25 rifampicin
pncA 2289081 p.Pro54Leu missense_variant 0.15 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.16 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 0.84
gyrA 7892 c.591G>A synonymous_variant 0.83
gyrA 9304 p.Gly668Asp missense_variant 0.81
mshA 576400 c.1053C>T synonymous_variant 0.16
ccsA 620029 c.139C>T synonymous_variant 0.9
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 0.78
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475395 n.1738T>C non_coding_transcript_exon_variant 0.86
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169991 p.Gly208Ser missense_variant 0.74
PPE35 2170048 p.Leu189Val missense_variant 0.27
PPE35 2170053 p.Thr187Ser missense_variant 0.25
PPE35 2170568 p.Ile15Met missense_variant 0.77
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3087367 p.Ala183Val missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.87
rpoA 3877536 c.972C>T synonymous_variant 0.12
clpC1 4038318 p.Pro796Leu missense_variant 0.83
embA 4242643 c.-590C>T upstream_gene_variant 0.86
ubiA 4269124 p.Ala237Val missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407967 p.Leu79Trp missense_variant 0.9