TB-Profiler result

Run: SRR19276639
Summary

Run ID: SRR19276639

Sample name:

Date: 03-04-2023 21:05:58

Number of reads: 3258868

Percentage reads mapped: 99.69

Strain: lineage4.3.3

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
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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.05
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.11
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
fabG1 1673423 c.-17G>T upstream_gene_variant 0.86 isoniazid, ethionamide
pncA 2289099 p.Lys48Thr missense_variant 0.1 pyrazinamide
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 8040 p.Gly247Ser missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761889 p.Val695Leu missense_variant 0.93
rpoC 764995 c.1626C>G synonymous_variant 0.12
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 0.89
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065517 c.675C>T synonymous_variant 0.92
Rv3083 3448439 c.-64delA upstream_gene_variant 0.9
fprA 3474299 p.Asp98Gly missense_variant 0.85
fbiA 3640372 c.-171A>G upstream_gene_variant 0.32
rpoA 3878636 c.-132C>G upstream_gene_variant 0.13
embC 4242182 p.Ala774Ser missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243392 p.Asn54Asp missense_variant 0.14
ubiA 4269731 p.Ala35Ser missense_variant 0.13
ethA 4328317 c.-844C>T upstream_gene_variant 0.96
whiB6 4338205 c.316dupG frameshift_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0