TB-Profiler result

Run: SRR5153215
Summary

Run ID: SRR5153215

Sample name:

Date: 04-04-2023 09:15:20

Number of reads: 959491

Percentage reads mapped: 99.08

Strain: lineage2

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 0.11
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 761095 p.Leu430Pro missense_variant 0.25 rifampicin
rpoB 761139 p.His445Asn missense_variant 0.2 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.8 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.56 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
tlyA 1918499 c.564delG frameshift_variant 0.67 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289030 p.His71Arg missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247513 p.Tyr334His 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 5410 c.171G>A synonymous_variant 0.25
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 9341 c.2040C>G synonymous_variant 0.33
fgd1 490782 c.-1G>A upstream_gene_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620243 p.Cys118Phe missense_variant 0.5
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.86
rpoC 765361 c.1993delG frameshift_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779252 p.Asp88Ala missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303972 p.Gly348Cys missense_variant 0.33
fbiC 1305220 p.Arg764Ser missense_variant 0.5
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407254 c.87G>T synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101989 p.Ala352Ser missense_variant 0.2
katG 2155907 p.Ala69Ser missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170392 p.Gly74Val missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714723 c.609delA frameshift_variant 0.67
ahpC 2726410 c.219_220delCG frameshift_variant 0.4
pepQ 2860107 c.312G>T synonymous_variant 0.29
ald 3087532 p.Ala238Asp missense_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.75
Rv3236c 3613280 c.-164G>T upstream_gene_variant 0.4
fbiB 3641127 c.-408T>C upstream_gene_variant 0.2
fbiB 3642354 p.Asp274Asn missense_variant 0.33
rpoA 3878093 p.Val139Ile missense_variant 0.4
embC 4240526 p.Tyr222His missense_variant 0.17
embC 4240586 p.Gly242Ser missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243193 c.-39delC upstream_gene_variant 0.25
embA 4243339 p.Val36Ala missense_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244459 c.1227G>A synonymous_variant 0.22
embA 4244708 c.1476C>A synonymous_variant 0.5
embB 4247344 c.831C>A synonymous_variant 0.22
embB 4247419 p.Tyr302* stop_gained 0.25
aftB 4267033 p.Ile602Val missense_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269622 p.Leu71Arg missense_variant 0.5
ethR 4327722 p.Arg58Ser missense_variant 0.22
whiB6 4338371 p.Thr51Pro missense_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 0.9