TB-Profiler result

Run: SRR6485010

Summary

Run ID: SRR6485010

Sample name:

Date: 04-04-2023 15:00:36

Number of reads: 4989633

Percentage reads mapped: 97.48

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 0.99 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2288924 c.317delT frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 0.97 ethambutol
ethA 4327480 c.-7T>C upstream_gene_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
fgd1 491100 c.318C>T synonymous_variant 0.13
fgd1 491106 c.324T>C synonymous_variant 0.15
fgd1 491121 c.339A>G synonymous_variant 0.15
fgd1 491130 c.348C>G synonymous_variant 0.17
fgd1 491144 p.Ala121Asp missense_variant 0.16
fgd1 491151 c.369G>A synonymous_variant 0.15
fgd1 491173 c.391C>A synonymous_variant 0.16
fgd1 491181 c.399T>C synonymous_variant 0.12
fgd1 491184 c.402A>G synonymous_variant 0.12
fgd1 491191 p.Gly137Arg missense_variant 0.12
fgd1 491194 c.412_414delCTAinsTTG synonymous_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 760834 p.His343Arg missense_variant 0.7
rpoB 761570 c.1764T>C synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 0.97
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 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.13
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.19
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.22
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 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>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
rpoA 3878322 c.186A>G synonymous_variant 0.11
rpoA 3878376 c.132G>C synonymous_variant 0.11
rpoA 3878385 c.123C>G synonymous_variant 0.11
rpoA 3878391 c.117T>C synonymous_variant 0.11
rpoA 3878424 c.84G>C synonymous_variant 0.11
rpoA 3878436 c.72A>G synonymous_variant 0.11
rpoA 3878442 c.66G>C synonymous_variant 0.11
rpoA 3878454 c.54A>C synonymous_variant 0.12
rpoA 3878484 c.24C>A synonymous_variant 0.13
rpoA 3878490 c.18C>A synonymous_variant 0.14
rpoA 3878496 c.12A>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.24
embB 4246556 p.Ala15Pro missense_variant 0.24
embB 4246563 p.Leu17Trp missense_variant 0.13
embB 4246567 c.54G>T synonymous_variant 0.13
embB 4246584 p.Arg24Pro missense_variant 0.28
aftB 4267647 p.Asp397Gly missense_variant 0.98
whiB6 4338563 c.-42G>T upstream_gene_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