TB-Profiler result

Run: SRR023451

Summary

Run ID: SRR023451

Sample name:

Date: 02-04-2023 14:12:08

Number of reads: 6435782

Percentage reads mapped: 90.08

Strain: lineage2.2.1

Drug-resistance: RR-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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
embB 4247643 p.Val377Gly missense_variant 0.33 ethambutol
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 0.99
fgd1 491324 p.Val181Gly missense_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576521 p.Gly392Trp missense_variant 0.2
ccsA 620088 p.Asp66Glu missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759831 p.Thr9Pro missense_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764916 p.Leu516Pro missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.97
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 0.98
fbiC 1304071 p.Thr381Pro missense_variant 0.27
Rv1258c 1406760 c.580_581insC frameshift_variant 0.97
embR 1417501 c.-154A>C upstream_gene_variant 0.2
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
tlyA 1918058 p.Val40Gly missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169971 c.642T>G synonymous_variant 0.22
Rv1979c 2221889 p.Val426Ile missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518163 p.Thr17Pro missense_variant 0.29
kasA 2518300 c.186T>G synonymous_variant 0.22
eis 2715087 c.246C>T synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642489 p.Ser319Ala missense_variant 0.19
alr 3841115 c.306T>G synonymous_variant 0.18
panD 4044471 c.-190T>G upstream_gene_variant 0.2
embC 4240646 p.Phe262Val missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244187 p.Thr319Pro missense_variant 0.26
embA 4244605 p.Val458Gly missense_variant 0.28
embA 4246085 p.Glu951Asp missense_variant 1.0
embB 4247822 p.Thr437Pro missense_variant 0.44
embB 4248663 p.Val717Gly missense_variant 0.26
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338536 c.-15G>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0