TB-Profiler result

Run: SRR6511608
Summary

Run ID: SRR6511608

Sample name:

Date: 04-04-2023 15:14:53

Number of reads: 462657

Percentage reads mapped: 99.44

Strain: lineage2.2

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 0.99
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethR 4327831 p.Ala95Thr missense_variant 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9676 p.Arg792His missense_variant 0.2
fgd1 490600 c.-183C>T upstream_gene_variant 0.13
fgd1 491345 p.Ala188Val missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575345 c.-3A>T upstream_gene_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576422 p.Ala359Thr missense_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620759 p.Arg290His missense_variant 0.17
rpoB 760177 p.Ala124Val missense_variant 0.12
rpoB 761279 c.1473C>T synonymous_variant 0.12
rpoB 761912 c.2106T>C synonymous_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 763725 p.Asp119Gly missense_variant 0.14
rpoC 763731 p.Ala121Val missense_variant 0.17
rpoC 765196 c.1827T>C synonymous_variant 0.12
rpoC 766699 p.Gln1110His 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
mmpL5 778048 p.Lys145Glu missense_variant 0.12
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779529 c.-624G>A upstream_gene_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801405 c.597T>C synonymous_variant 0.17
fbiC 1303126 p.Arg66Cys missense_variant 0.5
Rv1258c 1406256 p.Leu362* stop_gained 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416480 p.Ala290Thr missense_variant 0.13
embR 1417061 p.Ala96Gly missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472319 n.474C>T non_coding_transcript_exon_variant 0.12
rrs 1472638 n.793A>G non_coding_transcript_exon_variant 0.12
inhA 1673541 c.-661G>A upstream_gene_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
ndh 2103188 c.-146T>C upstream_gene_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155016 p.Asp366Asn missense_variant 0.43
katG 2155484 p.Tyr210Asn missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169960 p.Gly218Asp missense_variant 0.29
PPE35 2170699 c.-87C>G upstream_gene_variant 0.11
Rv1979c 2221945 p.Val407Gly missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519003 c.889C>T synonymous_variant 0.22
eis 2714963 p.Gly124Ser missense_variant 0.22
ahpC 2726728 p.Arg179His missense_variant 0.12
pepQ 2859761 p.Ile220Phe missense_variant 0.22
pepQ 2859789 c.630G>A synonymous_variant 0.15
Rv2752c 3065265 c.927C>T synonymous_variant 0.18
Rv2752c 3065434 c.757delG frameshift_variant 0.17
Rv2752c 3065722 p.Ala157Val missense_variant 0.22
Rv2752c 3065766 c.426G>A synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339397 p.Thr94Ala missense_variant 0.14
Rv3083 3449087 p.Ala195Val missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474218 p.Ala71Val missense_variant 0.13
fprA 3474320 p.Gly105Asp missense_variant 0.2
fprA 3475368 c.1362G>A synonymous_variant 0.14
whiB7 3568592 p.Ala30Thr missense_variant 0.15
whiB7 3568776 c.-97G>A upstream_gene_variant 0.11
Rv3236c 3612270 p.Asp283His missense_variant 0.1
Rv3236c 3612650 p.Val156Glu missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641754 p.Arg74Gly missense_variant 0.14
ddn 3987016 p.Gln58Arg missense_variant 0.12
clpC1 4038282 p.Asp808Val missense_variant 0.29
clpC1 4039411 p.Arg432Gly missense_variant 0.14
clpC1 4040073 p.Asn211Ile missense_variant 0.11
embC 4240943 p.Arg361Cys missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243024 c.-209T>C upstream_gene_variant 0.17
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243541 c.309C>T synonymous_variant 0.5
embA 4244906 c.1674C>T synonymous_variant 0.18
embA 4245340 p.Gly703Asp missense_variant 0.13
embA 4246429 p.Ala1066Val missense_variant 0.2
embB 4247521 c.1008G>A synonymous_variant 0.2
embB 4248317 p.Val602Ile missense_variant 0.11
embB 4248440 c.1929delC frameshift_variant 0.14
embB 4248756 p.Gly748Ala missense_variant 0.29
embB 4249592 p.Thr1027Ser missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267872 p.Gln322Arg missense_variant 0.33
aftB 4268299 p.Gly180Arg missense_variant 0.4
aftB 4268674 p.Val55Ile missense_variant 0.15
ubiA 4269682 p.Val51Ala missense_variant 0.18
ethA 4326066 p.Arg470Cys missense_variant 0.12
ethA 4327481 c.-8G>A upstream_gene_variant 0.13
ethA 4328401 c.-928G>A upstream_gene_variant 0.33
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 4408338 c.-136A>G upstream_gene_variant 0.15