TB-Profiler result

Run: ERR1034720
Summary

Run ID: ERR1034720

Sample name:

Date: 31-03-2023 09:36:15

Number of reads: 20816069

Percentage reads mapped: 99.63

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
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.4 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.99 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 0.99 isoniazid, ethionamide
pncA 2289010 p.Gly78Cys missense_variant 0.99 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.25 kanamycin
embB 4247574 p.Asp354Ala missense_variant 0.23 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 9304 p.Gly668Asp missense_variant 1.0
rpoB 761889 p.Val695Leu missense_variant 1.0
rpoC 764667 p.Gly433Asp missense_variant 0.17
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.25
PPE35 2169866 c.747G>C synonymous_variant 0.2
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065517 c.675C>T synonymous_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.33
Rv3083 3448439 c.-64delA upstream_gene_variant 1.0
fprA 3474299 p.Asp98Gly missense_variant 0.99
whiB7 3568840 c.-161A>G upstream_gene_variant 0.35
rpoA 3878595 c.-88C>T upstream_gene_variant 0.3
rpoA 3878635 c.-128C>T upstream_gene_variant 0.27
embC 4242425 p.Arg855Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.25
aftB 4268279 c.558G>A synonymous_variant 1.0
ubiA 4269148 p.Val229Ala missense_variant 0.74
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0