TB-Profiler result

Run: SRR1723955
Summary

Run ID: SRR1723955

Sample name:

Date: 17-08-2022 18:12:43

Number of reads: 2704931

Percentage reads mapped: 98.72

Strain: lineage4.5

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
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
lineage4.5 Euro-American H;T RD122 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
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2154973 p.Thr380Ile missense_variant 1.0 isoniazid
pncA 2288878 p.Gln122* stop_gained 1.0 pyrazinamide
ahpC 2726139 c.-54C>T upstream_gene_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576056 p.Val237Arg missense_variant 0.65
rpoB 762489 p.Val895Phe missense_variant 0.21
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 767314 p.Tyr1315* stop_gained 0.43
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
pncA 2290077 c.-836G>T upstream_gene_variant 1.0
thyA 3074465 p.Pro3Ala missense_variant 0.12
ald 3087860 c.1041A>G synonymous_variant 0.92
alr 3841364 c.57C>T synonymous_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0