TB-Profiler result

Run: SRR15316526

Summary

Run ID: SRR15316526

Sample name:

Date: 03-04-2023 13:36:50

Number of reads: 9942697

Percentage reads mapped: 99.56

Strain: lineage4;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.93
lineage4 Euro-American LAM;T;S;X;H None 0.07
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.93
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.93
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 0.91 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.96 isoniazid, ethionamide
katG 2155729 c.382dupC frameshift_variant 0.93 isoniazid
katG 2155740 c.371delG frameshift_variant 0.94 isoniazid, isoniazid
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
fgd1 491742 c.960T>C synonymous_variant 0.94
mshA 575907 p.Ala187Val missense_variant 0.93
ccsA 620625 p.Ile245Met missense_variant 0.95
rpoB 761467 p.Leu554Pro missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 0.9
rpoC 764817 p.Val483Ala missense_variant 0.59
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.92
mmpS5 779615 c.-710C>G upstream_gene_variant 0.93
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.95
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.95
PPE35 2167926 p.Leu896Ser missense_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726077 c.-116T>C upstream_gene_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 0.91
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.92
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.89
aftB 4266967 p.Pro624Thr missense_variant 0.91
aftB 4267647 p.Asp397Gly missense_variant 0.95
ubiA 4269299 p.Ile179Val missense_variant 0.7
ubiA 4269311 p.Trp175Gly missense_variant 0.25
whiB6 4338286 p.Val79Gly missense_variant 0.9
whiB6 4338292 p.Ala77Glu missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407927 p.Glu92Asp missense_variant 0.93