TB-Profiler result

Run: SRR998830
Summary

Run ID: SRR998830

Sample name:

Date: 04-04-2023 23:38:15

Number of reads: 3193983

Percentage reads mapped: 99.37

Strain: lineage4.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.3 Euro-American T;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 761139 p.His445Asp missense_variant 0.74 rifampicin
rpoB 761155 p.Ser450Phe missense_variant 0.26 rifampicin
fabG1 1673432 c.-8T>C upstream_gene_variant 0.74 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288832 p.His137Arg missense_variant 0.23 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.18 ethambutol
gid 4407967 p.Leu79Ser missense_variant 0.83 streptomycin
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 0.98
gyrA 9557 c.2256G>C synonymous_variant 0.85
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
fbiC 1304610 c.1680C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674102 c.-100C>A upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ubiA 4269313 p.Lys174Thr missense_variant 0.16
ethA 4327471 c.1_3delATGinsCTT start_lost 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 0.9