TB-Profiler result

Run: SRR13068984
Summary

Run ID: SRR13068984

Sample name:

Date: 03-04-2023 08:12:11

Number of reads: 103957

Percentage reads mapped: 99.34

Strain: lineage4

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.84
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 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 6676 c.-626T>G upstream_gene_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155106 p.Leu336Met missense_variant 0.22
PPE35 2167663 p.Ser984Gly missense_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221865 p.Tyr434His missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289760 c.-519C>T upstream_gene_variant 1.0
eis 2714432 p.Val301Ile missense_variant 1.0
ahpC 2726710 p.Leu173Pro missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267130 c.1707C>A synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268285 c.552A>G synonymous_variant 1.0
ethA 4327110 p.Ser122Gly missense_variant 0.17
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0