TB-Profiler result

Run: ERR1034680
Summary

Run ID: ERR1034680

Sample name:

Date: 20-10-2023 21:51:40

Number of reads: 5642518

Percentage reads mapped: 99.58

Strain: lineage4.3.4.1;lineage4.1.2.1

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.Asp435Val (0.84), rpoB p.Ser450Leu (0.17), rpoC p.Gly332Arg (0.26)
Isoniazid R fabG1 c.-15C>T (1.00), katG p.Ser315Thr (0.87)
Ethambutol R embB p.Met306Val (0.15)
Pyrazinamide R pncA c.-11A>G (0.16)
Streptomycin R rpsL p.Lys43Arg (0.11), gid p.Leu79Ser (0.87)
Fluoroquinolones R gyrA p.Asp94Gly (0.18)
Moxifloxacin R gyrA p.Asp94Gly (0.18)
Ofloxacin R gyrA p.Asp94Gly (0.18)
Levofloxacin R gyrA p.Asp94Gly (0.18)
Ciprofloxacin R gyrA p.Asp94Gly (0.18)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
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 0.87
lineage4.1 Euro-American T;X;H None 0.12
lineage4.1.2 Euro-American T;H None 0.11
lineage4.3.4 Euro-American (LAM) LAM RD174 0.88
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.13
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.89
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 7582 p.Asp94Gly missense_variant 0.18 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.84 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.17 rifampicin
rpoC 764363 p.Gly332Arg missense_variant 0.26 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.11 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155167 p.Ser315Thr missense_variant 0.87 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.16 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.15 ethambutol
gid 4407967 p.Leu79Ser missense_variant 0.87 streptomycin
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 7587 c.286C>T synonymous_variant 0.19
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 0.16
rpoC 764863 c.1494G>C synonymous_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 0.85
rpoC 766628 p.Arg1087Gly missense_variant 0.13
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.15
ahpC 2726323 p.Pro44Arg missense_variant 0.86
ribD 2986729 c.-110G>A upstream_gene_variant 0.92
thyA 3073868 p.Thr202Ala missense_variant 0.84
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.83
clpC1 4038287 c.2418C>T synonymous_variant 0.87
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269133 p.Gly234Val missense_variant 0.89
ubiA 4269296 p.Met180Val missense_variant 0.14
ethA 4326344 p.Ile377Ser missense_variant 0.13
whiB6 4338594 c.-75_-73delGCTinsCC upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.84