TB-Profiler result

Run: ERR3287581
Summary

Run ID: ERR3287581

Sample name:

Date: 01-04-2023 01:31:31

Number of reads: 3529962

Percentage reads mapped: 99.73

Strain: lineage4

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
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
tlyA 1918207 c.271_272dupGC frameshift_variant 0.11 capreomycin
tlyA 1918218 c.281dupG frameshift_variant 0.13 capreomycin
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.84 ethambutol
ethA 4326718 c.754_755dupGC frameshift_variant 0.39 ethionamide, ethionamide
ethA 4327411 c.61_62delTG frameshift_variant 0.27 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 7581 p.Asp94Arg missense_variant 0.53
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
rpoB 761008 p.Gln401Arg missense_variant 0.12
rpoB 761889 p.Val695Leu missense_variant 1.0
rpoC 766467 p.Glu1033Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472548 n.703A>C non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154415 p.Pro566Arg missense_variant 1.0
katG 2155822 p.His97Arg missense_variant 0.97
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859978 p.Cys147* stop_gained 0.11
Rv2752c 3065517 c.675C>T synonymous_variant 1.0
Rv3083 3449649 c.1146C>T synonymous_variant 1.0
fprA 3474299 p.Asp98Gly missense_variant 1.0
rpoA 3878580 c.-73A>C upstream_gene_variant 0.1
rpoA 3878595 c.-88C>T upstream_gene_variant 0.33
rpoA 3878635 c.-128C>T upstream_gene_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326737 p.Gln246Arg missense_variant 0.28
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407928 p.Glu92Gly missense_variant 1.0