TB-Profiler result

Run: SRR6832756
Summary

Run ID: SRR6832756

Sample name:

Date: 04-04-2023 17:37:34

Number of reads: 1730773

Percentage reads mapped: 99.26

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
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247469 p.Tyr319Ser 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 8502 p.Leu401Met missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490787 p.Ala2Asp missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761326 p.Glu507Gly missense_variant 1.0
rpoB 761331 p.Pro509Thr missense_variant 0.11
rpoB 761852 c.2046C>A synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766197 p.Asp943Gly missense_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
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 1.0
Rv1258c 1406266 p.Ala359Ser missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673602 p.Leu55Met missense_variant 0.12
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
katG 2155008 p.Phe368Leu missense_variant 0.2
katG 2155023 c.1089C>A synonymous_variant 0.18
katG 2155295 p.Gly273Cys missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2725919 c.-274A>G upstream_gene_variant 0.11
folC 2747051 p.Ala183Asp missense_variant 0.13
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473952 c.-55C>A upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474599 p.Gly198Val missense_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642066 p.Gly178Ser missense_variant 0.2
fbiB 3642343 p.Pro270Gln missense_variant 0.15
alr 3840302 p.Glu373Asp missense_variant 0.15
embC 4240198 p.Gln112His missense_variant 0.12
embC 4241307 p.Val482Asp missense_variant 0.15
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 4246655 p.Pro48Ala missense_variant 0.1
embB 4247046 c.537dupC frameshift_variant 0.18
embB 4247598 p.Trp362* stop_gained 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269082 p.Ser251Leu missense_variant 0.11
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
gid 4408359 c.-157G>C upstream_gene_variant 0.1