TB-Profiler result

Run: ERR2706912
Summary

Run ID: ERR2706912

Sample name:

Date: 19-10-2023 12:06:02

Number of reads: 4032835

Percentage reads mapped: 99.58

Strain: lineage4.6.1.1;lineage4.3.4.2;lineage4.3.3

Drug-resistance: RR-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 (0.14)
Isoniazid
Ethambutol R embB p.Met306Val (0.15)
Pyrazinamide R pncA p.Leu19Pro (0.15)
Streptomycin R rpsL p.Lys43Arg (0.10)
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 0.71
lineage4.6 Euro-American T;LAM None 0.24
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.63
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.24
lineage4.3.4 Euro-American (LAM) LAM RD174 0.08
lineage4.6.1.1 Euro-American T2-Uganda RD724 0.21
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.1
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 0.14 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.1 streptomycin
pncA 2289186 p.Leu19Pro missense_variant 0.15 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.15 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 5723 p.Ala162Ser missense_variant 0.63
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 0.94
gyrA 8040 p.Gly247Ser missense_variant 0.66
gyrA 9304 p.Gly668Asp missense_variant 0.97
mshA 575240 c.-108G>A upstream_gene_variant 0.63
rpoC 764840 p.Ile491Val missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 0.77
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
katG 2155566 c.546G>T synonymous_variant 0.6
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.63
thyA 3073868 p.Thr202Ala missense_variant 0.75
ald 3086788 c.-32T>C upstream_gene_variant 0.74
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
clpC1 4038287 c.2418C>T synonymous_variant 0.76
embC 4242182 p.Ala774Ser missense_variant 0.68
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328329 c.-856C>G upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.72