TB-Profiler result

Run: SRR11972287
Summary

Run ID: SRR11972287

Sample name:

Date: 03-04-2023 05:34:46

Number of reads: 701469

Percentage reads mapped: 99.39

Strain: lineage2.2.2

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 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4249583 p.Asp1024Asn 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
gyrB 6773 p.Gly512Arg missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7381 p.Ser27Asn missense_variant 0.11
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7720 p.Glu140Val missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491082 c.300T>C synonymous_variant 0.15
fgd1 491576 p.Pro265Gln missense_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763323 c.3517T>C stop_lost&splice_region_variant 0.1
rpoC 764363 p.Gly332Cys missense_variant 1.0
rpoC 764769 p.Gln467Arg missense_variant 0.12
rpoC 765823 c.2454C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776217 p.Ala755Val missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781567 p.Thr3Asn missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834745 p.Glu402Lys missense_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 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715440 c.-108A>C upstream_gene_variant 0.1
eis 2715450 c.-118T>C upstream_gene_variant 0.1
eis 2715454 c.-122T>G upstream_gene_variant 0.1
eis 2715460 c.-128A>G upstream_gene_variant 0.1
eis 2715465 c.-133G>T upstream_gene_variant 0.11
eis 2715469 c.-137T>C upstream_gene_variant 0.11
eis 2715473 c.-141A>G upstream_gene_variant 0.11
Rv2752c 3065069 p.His375Tyr missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086918 c.99G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474602 p.Arg199Leu missense_variant 0.17
fprA 3475228 p.Asp408Asn missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641681 c.147C>A synonymous_variant 0.15
alr 3841419 p.Val1Gly missense_variant 1.0
embC 4241693 p.Ala611Thr missense_variant 0.15
embC 4242420 p.Ser853Thr missense_variant 0.29
embC 4242421 c.2562_2580delGCGAGCCGGCGTGCAGGTG frameshift_variant 0.29
embC 4242444 p.Pro861His missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245155 c.1923C>T synonymous_variant 0.17
embB 4245851 c.-663G>A upstream_gene_variant 1.0
embA 4246002 p.Asn924Tyr missense_variant 0.15
embA 4246334 p.Gln1034His missense_variant 1.0
embB 4249500 p.Cys996Tyr missense_variant 0.11
aftB 4267647 p.Asp397Gly 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