TB-Profiler result

Run: SRR1002690
Summary

Run ID: SRR1002690

Sample name:

Date: 02-04-2023 14:19:55

Number of reads: 813732

Percentage reads mapped: 95.21

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 0.97
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.98
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 0.93 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embA 4243221 c.-12C>T upstream_gene_variant 0.9 ethambutol
embB 4247399 p.Asn296His missense_variant 1.0 ethambutol
ethA 4327363 c.110delA frameshift_variant 1.0 ethionamide, ethionamide
pncA 2288778 c.-541_463del frameshift_variant&start_lost 1.0 pyrazinamide
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 0.9
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619901 p.Leu4Pro missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
rpoC 764817 p.Val483Gly 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 0.96
mmpR5 779323 p.Ala112Thr missense_variant 0.15
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
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
katG 2156083 p.Glu10Gly missense_variant 0.94
katG 2156374 c.-263A>G upstream_gene_variant 0.38
PPE35 2167814 c.2799C>T synonymous_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.16
PPE35 2167868 c.2745A>C synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.16
PPE35 2169272 c.1341C>G synonymous_variant 0.15
PPE35 2169598 p.Phe339Val missense_variant 0.1
PPE35 2169902 p.Leu237Phe missense_variant 0.23
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2170147 p.Ser156Ala missense_variant 0.18
PPE35 2170159 p.Ala152Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519140 c.1026G>C synonymous_variant 0.23
kasA 2519143 c.1029G>C synonymous_variant 0.24
kasA 2519153 p.Ile347Val missense_variant 0.1
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449154 c.653delT frameshift_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.94
fbiA 3641485 p.Ala315Thr missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.17
embC 4240801 c.939C>T synonymous_variant 0.25
embC 4240803 p.Tyr314Phe missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.95
embA 4244977 p.Gly582Val missense_variant 0.13
embA 4246291 c.3060delA frameshift_variant 0.11
embB 4247426 p.Gly305Thr missense_variant 0.2
embB 4249779 p.Trp1089Ser missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4327772 p.Leu75Pro missense_variant 0.11
whiB6 4338371 p.Thr51Pro missense_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.86
gid 4407927 p.Glu92Asp missense_variant 1.0