TB-Profiler result

Run: ERR4799949

Summary

Run ID: ERR4799949

Sample name:

Date: 20-10-2023 04:05:09

Number of reads: 2923860

Percentage reads mapped: 99.43

Strain: lineage4.2.2.2

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.Ser315Thr (1.00)
Ethambutol R embB p.Gln497Arg (0.96)
Pyrazinamide R pncA p.Pro62Leu (0.98)
Streptomycin R rpsL p.Lys43Arg (0.98)
Fluoroquinolones R gyrA p.Asp94Gly (0.98)
Moxifloxacin R gyrA p.Asp94Gly (0.98)
Ofloxacin R gyrA p.Asp94Gly (0.98)
Levofloxacin R gyrA p.Asp94Gly (0.98)
Ciprofloxacin R gyrA p.Asp94Gly (0.98)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA p.Ser390Phe (0.95)
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 0.97
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.96
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.97
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 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289057 p.Pro62Leu missense_variant 0.98 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.96 ethambutol
ethA 4326305 p.Ser390Phe missense_variant 0.95 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 1.0
gyrA 8688 p.Ala463Ser missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 0.99
rpoB 761489 c.1683G>A synonymous_variant 0.98
rpoC 764840 p.Ile491Val missense_variant 0.34
rpoC 765842 p.Thr825Ser missense_variant 0.21
rpoC 766485 p.Val1039Gly missense_variant 0.38
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 0.93
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.97
ald 3086742 c.-78A>C upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449395 p.Cys298Arg missense_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240327 c.465G>A synonymous_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0