TB-Profiler result

Run: SRR15369010
Summary

Run ID: SRR15369010

Sample name:

Date: 03-04-2023 14:05:29

Number of reads: 6543033

Percentage reads mapped: 84.63

Strain: lineage4.5;lineage2.2.1.1

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
lineage2 East-Asian Beijing RD105 0.8
lineage4 Euro-American LAM;T;S;X;H None 0.21
lineage4.5 Euro-American H;T RD122 0.21
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.82
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.79
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.81
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 1673425 c.-15C>T upstream_gene_variant 0.24 isoniazid, 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 0.21
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.83
mshA 575907 p.Ala187Val missense_variant 0.8
ccsA 620029 c.139C>T synonymous_variant 0.23
ccsA 620625 p.Ile245Met missense_variant 0.79
rpoC 763031 c.-339T>C upstream_gene_variant 0.8
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.79
mmpL5 776182 p.Asp767Asn missense_variant 0.78
mmpL5 776964 p.Thr506Ile missense_variant 0.73
mmpS5 779615 c.-710C>G upstream_gene_variant 0.81
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303026 c.96G>A synonymous_variant 0.21
Rv1258c 1406760 c.580_581insC frameshift_variant 0.8
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833734 p.Ala65Thr missense_variant 0.21
rpsA 1834177 c.636A>C synonymous_variant 0.75
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.8
PPE35 2167926 p.Leu896Ser missense_variant 0.79
PPE35 2168605 p.Pro670Ser missense_variant 0.23
PPE35 2170568 p.Ile15Met missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518871 p.His253Tyr missense_variant 0.8
eis 2714211 c.1122G>A synonymous_variant 0.23
eis 2714846 p.Val163Ile missense_variant 0.86
ald 3086788 c.-32T>C upstream_gene_variant 0.81
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.8
rpoA 3878575 c.-68C>T upstream_gene_variant 0.14
clpC1 4038318 p.Pro796Leu missense_variant 0.2
clpC1 4040654 c.51G>A synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.77
embB 4248115 c.1602C>T synonymous_variant 0.81
aftB 4267647 p.Asp397Gly missense_variant 0.81
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338646 c.-125A>G upstream_gene_variant 0.81
gid 4407588 c.615A>G synonymous_variant 0.75
gid 4407927 p.Glu92Asp missense_variant 0.76