TB-Profiler result

Run: ERR5864956

Summary

Run ID: ERR5864956

Sample name:

Date: 01-04-2023 23:42:12

Number of reads: 1220165

Percentage reads mapped: 98.69

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 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289030 p.His71Pro missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 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 1.0
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 759830 p.Lys8Asn missense_variant 0.13
rpoB 761857 c.2053delG frameshift_variant 0.12
rpoB 762069 p.Asp755His missense_variant 0.11
rpoC 762764 c.-606G>T upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764833 p.Glu488Asp missense_variant 0.94
rpoC 764868 p.Arg500His missense_variant 0.12
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766740 p.Val1124Gly missense_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
mmpS5 778602 c.303delC frameshift_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303349 p.Cys140Tyr missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473014 n.1169G>A non_coding_transcript_exon_variant 0.11
inhA 1674718 p.Arg173Trp missense_variant 0.14
inhA 1674933 c.732G>T synonymous_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917921 c.-19G>T upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154631 p.Gly494Asp missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.11
PPE35 2170053 p.Thr187Ser missense_variant 0.11
PPE35 2170066 p.Ala183Thr missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289705 c.-464G>T upstream_gene_variant 0.11
kasA 2518526 c.416delC frameshift_variant 0.14
pepQ 2859886 p.Ala178Gly missense_variant 0.13
ribD 2987587 c.751delC frameshift_variant 0.11
Rv2752c 3065115 c.1077C>T synonymous_variant 0.11
Rv2752c 3065727 c.465C>T synonymous_variant 0.13
Rv2752c 3067119 c.-928C>A upstream_gene_variant 0.13
Rv2752c 3067141 c.-950A>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
fprA 3474918 c.912C>T synonymous_variant 0.12
fprA 3475198 p.Phe398Leu missense_variant 0.11
fprA 3475336 p.Leu444Met missense_variant 0.12
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245736 p.Ala835Glu missense_variant 0.1
embB 4247944 c.1431G>T synonymous_variant 0.11
embB 4249534 c.3021C>T synonymous_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267814 c.1023G>A synonymous_variant 0.22
aftB 4269576 c.-740C>T upstream_gene_variant 0.13
ubiA 4269667 p.Ser56Trp missense_variant 0.11
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