TB-Profiler result

Run: ERR4830157
Summary

Run ID: ERR4830157

Sample name:

Date: 20-10-2023 01:34:32

Number of reads: 2201853

Percentage reads mapped: 99.65

Strain: lineage4.8;lineage4.5

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Arg (0.42), katG p.Gly121Val (0.41), ahpC c.-54C>T (0.41)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1401A>G (0.14)
Amikacin R rrs n.1401A>G (0.14)
Capreomycin R rrs n.1401A>G (0.14)
Kanamycin R rrs n.1401A>G (0.14)
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 0.42
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.63
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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.14 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155167 p.Ser315Arg missense_variant 0.42 isoniazid
katG 2155750 p.Gly121Val missense_variant 0.41 isoniazid
ahpC 2726139 c.-54C>T upstream_gene_variant 0.41 isoniazid
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 7293 c.-9G>T upstream_gene_variant 0.48
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.47
gyrA 7892 c.591G>A synonymous_variant 0.52
gyrA 8042 c.741C>T synonymous_variant 0.39
gyrA 9304 p.Gly668Asp missense_variant 0.39
ccsA 620029 c.139C>T synonymous_variant 0.35
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776371 p.Gly704Cys missense_variant 0.51
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 0.48
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.57
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155367 p.Arg249Ser missense_variant 0.16
PPE35 2170521 p.Trp31* stop_gained 0.39
PPE35 2170568 p.Ile15Met missense_variant 0.43
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3074585 c.-118_-115delGACT upstream_gene_variant 0.45
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.29
whiB7 3568581 c.98delC frameshift_variant 0.44
whiB7 3568734 c.-55G>A upstream_gene_variant 0.33
rpoA 3878575 c.-68C>T upstream_gene_variant 0.6
clpC1 4038318 p.Pro796Leu missense_variant 0.42
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246714 c.201G>T synonymous_variant 0.43
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407790 p.Ala138Val missense_variant 0.49
gid 4407853 p.Gly117Glu missense_variant 0.47