TB-Profiler result

Run: ERR4798869
Summary

Run ID: ERR4798869

Sample name:

Date: 20-10-2023 03:12:43

Number of reads: 2380042

Percentage reads mapped: 99.54

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.Gln432Leu (0.93)
Isoniazid R katG p.Ser315Thr (0.98)
Ethambutol R embB p.Met306Ile (0.97)
Pyrazinamide R pncA c.-11A>G (0.96)
Streptomycin R rpsL p.Lys43Arg (0.98)
Fluoroquinolones R gyrA p.Ala90Val (0.95)
Moxifloxacin R gyrA p.Ala90Val (0.95)
Ofloxacin R gyrA p.Ala90Val (0.95)
Levofloxacin R gyrA p.Ala90Val (0.95)
Ciprofloxacin R gyrA p.Ala90Val (0.95)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.951_1017delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNA (0.96)
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 0.99
lineage4.2 Euro-American H;T;LAM None 0.97
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.97
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.96
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 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761101 p.Gln432Leu missense_variant 0.93 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.96 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.97 ethambutol
ethA 4326456 c.951_1017delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNA frameshift_variant 0.96 ethionamide
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 0.98
gyrA 8688 p.Ala463Ser missense_variant 0.98
gyrA 9304 p.Gly668Asp missense_variant 0.93
mshA 576077 c.730C>T synonymous_variant 0.99
rpoB 761489 c.1683G>A synonymous_variant 0.9
rpoB 762286 p.Arg827His missense_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302927 c.-4C>T upstream_gene_variant 0.98
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
ribD 2986827 c.-12G>A upstream_gene_variant 0.97
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.99
ald 3086742 c.-78A>C upstream_gene_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473832 c.-175T>C upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
embC 4240327 c.465G>A synonymous_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0