TB-Profiler result

Run: ERR4827420
Summary

Run ID: ERR4827420

Sample name:

Date: 01-04-2023 18:02:09

Number of reads: 1144078

Percentage reads mapped: 95.96

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 0.95 rifampicin
rpoC 764724 p.Phe452Ser missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.56 pyrazinamide
embB 4247469 p.Tyr319Cys missense_variant 1.0 ethambutol
ethA 4327054 p.Tyr140* stop_gained 1.0 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 7581 p.Asp94Thr missense_variant 0.33
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 575371 p.Asp8Glu missense_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.19
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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 777257 c.1224G>T synonymous_variant 0.15
mmpS5 778632 c.267_273delGCTCACC frameshift_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304437 c.1508delA frameshift_variant 0.1
fbiC 1304442 c.1512T>C synonymous_variant 0.12
fbiC 1304443 p.Ala505Thr missense_variant 0.12
fbiC 1304446 c.1516_1517insT frameshift_variant 0.12
fbiC 1304988 c.2058G>A synonymous_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
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
PPE35 2168312 p.Gln767His missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.37
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860200 c.219G>A synonymous_variant 0.12
pepQ 2860201 c.216_217delAG frameshift_variant 0.12
pepQ 2860207 c.211_212insGCGCGC conservative_inframe_insertion 0.14
ald 3086731 c.-89A>G upstream_gene_variant 1.0
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
embA 4242259 c.-974G>C upstream_gene_variant 0.2
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 4246544 p.Thr11Pro missense_variant 0.41
embB 4246548 p.Pro12Gln missense_variant 0.44
embB 4246555 c.42G>C synonymous_variant 0.43
embB 4246556 p.Ala15Pro missense_variant 0.43
embB 4246563 p.Leu17Trp missense_variant 0.31
embB 4246567 c.54G>T synonymous_variant 0.31
aftB 4267647 p.Asp397Gly missense_variant 0.98
ubiA 4269298 p.Ile179Thr missense_variant 0.31
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