TB-Profiler result

Run: SRR13068986
Summary

Run ID: SRR13068986

Sample name:

Date: 03-04-2023 08:12:14

Number of reads: 109915

Percentage reads mapped: 99.35

Strain: lineage2

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 0.14
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288961 p.Phe94Ser missense_variant 1.0 pyrazinamide
ethA 4327211 p.Thr88Ile missense_variant 1.0 ethionamide
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9024 p.Arg575Trp missense_variant 0.67
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764844 p.Ala492Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777524 c.957T>G synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834159 c.618G>A synonymous_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103127 c.-85A>G upstream_gene_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168681 p.Phe644Leu missense_variant 0.5
PPE35 2170621 c.-9T>G upstream_gene_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747002 p.Ile199Met missense_variant 0.5
ribD 2986699 c.-140T>C upstream_gene_variant 1.0
Rv2752c 3065481 p.Cys237Trp missense_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087575 c.756T>C synonymous_variant 0.33
ald 3087617 c.798T>C synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4040389 p.Glu106* stop_gained 0.4
panD 4044348 c.-67G>A upstream_gene_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244025 p.His265Tyr missense_variant 0.22
embA 4245528 p.Gly766Ser missense_variant 0.25
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407923 c.280C>T synonymous_variant 0.4
gid 4407927 p.Glu92Asp missense_variant 1.0