TB-Profiler result

Run: ERR5863538

Summary

Run ID: ERR5863538

Sample name:

Date: 01-04-2023 22:44:21

Number of reads: 725085

Percentage reads mapped: 99.53

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.Ser450Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288820 p.Gln141Pro missense_variant 1.0 pyrazinamide
pncA 2289167 c.73_74dupGC frameshift_variant 0.15 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
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 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765978 p.Ser870Tyr missense_variant 0.15
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
fbiC 1302983 p.Pro18Leu missense_variant 0.12
fbiC 1303011 c.81G>A synonymous_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474974 n.1317G>A non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834624 c.1083G>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102276 p.Gly256Asp missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168005 p.His870Tyr missense_variant 0.12
PPE35 2168319 p.Thr765Asn missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714454 c.879C>T synonymous_variant 0.17
Rv2752c 3065150 c.1041_1042insA frameshift_variant 1.0
Rv2752c 3065844 c.348T>C synonymous_variant 0.11
Rv2752c 3067187 c.-997_-996insG upstream_gene_variant 1.0
thyA 3074358 c.114G>A synonymous_variant 0.18
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339000 c.-118_-117insCA upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612430 c.687G>A synonymous_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642065 c.531C>T synonymous_variant 0.25
fbiB 3642393 p.Pro287Ser missense_variant 0.18
clpC1 4038164 c.2538_2540delCGC disruptive_inframe_deletion 0.1
panD 4044010 p.Ala91Val missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.9
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243557 p.Ala109Thr missense_variant 0.12
embA 4244184 p.Ser318Leu missense_variant 0.18
embB 4247129 p.Ile206Phe missense_variant 0.29
embB 4247352 p.Asp280Gly missense_variant 0.13
embB 4248317 p.Val602Pro missense_variant 0.12
embB 4248320 p.Gly603Thr missense_variant 0.12
embB 4249410 p.Pro966Gln missense_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267831 c.1004_1005dupAC frameshift_variant 0.22
ethR 4327207 c.-342C>T upstream_gene_variant 0.12
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