TB-Profiler result

Run: SRR18715372
Summary

Run ID: SRR18715372

Sample name:

Date: 03-04-2023 20:31:25

Number of reads: 4315422

Percentage reads mapped: 99.56

Strain: lineage2.2.1

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289009 p.Gly78Asp missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4326770 c.703delT frameshift_variant 1.0 ethionamide, 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.31
mshA 576613 c.1266A>C synonymous_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764660 p.Val431Met missense_variant 0.35
rpoC 764820 p.Trp484Ser missense_variant 0.46
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.17
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
fabG1 1673553 p.Asp38Glu missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102417 p.Ala209Val missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2170065 p.Ala183Gly missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.22
pepQ 2860159 p.Ala87Gly missense_variant 0.17
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.71
fbiD 3339746 p.Ala210Gly missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 p.Gly84Ala missense_variant 0.45
Rv3236c 3612813 p.Thr102Ala missense_variant 0.98
rpoA 3878434 p.Pro25Arg missense_variant 0.19
rpoA 3878590 c.-83G>T upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.62
embC 4240409 p.Pro183Ala missense_variant 0.16
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
embB 4246584 p.Arg24Pro missense_variant 0.17
embB 4247016 p.Ser168Trp missense_variant 0.26
embB 4247033 p.Ser174Arg missense_variant 0.29
embB 4248328 c.1815G>C synonymous_variant 0.19
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338200 p.Asp108His missense_variant 0.16
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 4407927 p.Glu92Asp missense_variant 1.0