TB-Profiler result

Run: ERR4830821
Summary

Run ID: ERR4830821

Sample name:

Date: 20-10-2023 06:47:10

Number of reads: 4128253

Percentage reads mapped: 99.53

Strain: lineage4.2.2.2

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.His445Cys (0.86), rpoB p.Ser450Leu (0.17)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.84), embB p.Met306Ile (0.15)
Pyrazinamide R pncA c.-11A>G (0.19)
Streptomycin R gid p.Gly69Asp (0.17)
Fluoroquinolones R gyrA p.Ala90Val (0.83)
Moxifloxacin R gyrA p.Ala90Val (0.83)
Ofloxacin R gyrA p.Ala90Val (0.83)
Levofloxacin R gyrA p.Ala90Val (0.83)
Ciprofloxacin R gyrA p.Ala90Val (0.83)
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 0.99
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
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 0.83 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Cys missense_variant 0.86 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.17 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.19 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.84 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.15 ethambutol
gid 4407997 p.Gly69Asp missense_variant 0.17 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 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoC 764397 p.Leu343Arg missense_variant 0.74
rpoC 766488 p.Pro1040Arg missense_variant 0.12
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
tlyA 1918334 p.Glu132Val missense_variant 0.88
katG 2154710 p.Thr468Pro missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518546 p.Met144Ile missense_variant 0.82
ahpC 2726146 c.-47_-46insT upstream_gene_variant 0.16
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 1.0
Rv3083 3449623 c.1120_1121insT frameshift_variant 0.85
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249680 p.Asp1056Ala missense_variant 0.89
ethA 4326038 p.Arg479Pro missense_variant 0.81
ethA 4327472 c.2T>G start_lost 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407733 p.Gly157Val missense_variant 0.85