TB-Profiler result

Run: SRR14782490
Summary

Run ID: SRR14782490

Sample name:

Date: 03-04-2023 11:27:39

Number of reads: 1636236

Percentage reads mapped: 99.5

Strain: lineage2.2.1

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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
eis 2715342 c.-10G>A upstream_gene_variant 0.97 kanamycin
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 9034 p.Arg578Gln missense_variant 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.98
mshA 576113 p.Arg256Gly missense_variant 0.2
mshA 576446 p.Thr367Pro missense_variant 0.25
mshA 576456 p.Val370Gly missense_variant 0.24
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.18
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.98
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.19
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 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.23
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.21
pepQ 2860159 p.Ala87Gly missense_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.15
fbiD 3339734 p.Ala206Gly missense_variant 0.6
fbiD 3339749 p.Val211Gly missense_variant 0.4
fbiD 3339751 p.Ala212Pro missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.67
whiB7 3568428 c.252A>G synonymous_variant 0.71
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878558 c.-52_-51insG upstream_gene_variant 0.25
rpoA 3878563 c.-58_-57delGC upstream_gene_variant 0.4
rpoA 3878567 c.-60C>G upstream_gene_variant 0.6
rpoA 3878569 c.-63_-62insG upstream_gene_variant 1.0
rpoA 3878639 c.-132C>G upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.43
embC 4240409 p.Pro183Ala missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.43
embB 4246529 p.Ser6Arg missense_variant 0.43
embB 4248328 c.1815G>C synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338200 p.Asp108His missense_variant 0.13
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