TB-Profiler result

Run: SRR5526143

Summary

Run ID: SRR5526143

Sample name:

Date: 04-04-2023 10:35:01

Number of reads: 796614

Percentage reads mapped: 99.62

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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 491742 c.960T>C synonymous_variant 1.0
mshA 575451 p.Asn35Ile missense_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576295 c.948C>A synonymous_variant 0.17
mshA 576586 c.1239G>T synonymous_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_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
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304415 c.1485G>T synonymous_variant 0.12
fbiC 1304488 p.Ala520Thr missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918626 c.687G>T synonymous_variant 0.25
ndh 2102738 c.304delG frameshift_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 1.0
PPE35 2170053 p.Thr187Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 1.0
eis 2715029 p.Ala102Ser missense_variant 0.11
folC 2746436 p.Asp388Gly missense_variant 0.2
folC 2746458 p.Val381Leu missense_variant 0.2
folC 2746968 p.Gly211Arg missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339537 c.420C>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612051 p.Thr356Ala missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4241737 c.1875G>T synonymous_variant 0.22
embC 4242371 p.Ala837Thr missense_variant 0.25
embC 4242587 p.Gly909Arg missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245131 c.1899G>A synonymous_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267778 c.1059T>C synonymous_variant 0.12
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