TB-Profiler result

Run: SRR11972399
Summary

Run ID: SRR11972399

Sample name:

Date: 03-04-2023 05:40:18

Number of reads: 942678

Percentage reads mapped: 98.87

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 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 761140 p.His445Arg missense_variant 0.91 rifampicin
rrs 1472750 n.905C>G non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp 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
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 575865 p.Leu173* stop_gained 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.38
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.21
rpoB 759620 c.-187A>C upstream_gene_variant 0.19
rpoB 761581 p.Glu592Gly missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764058 p.Ala230Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775798 p.Phe895Leu missense_variant 0.11
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 1305453 c.2523C>T synonymous_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406810 c.531C>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834460 p.Phe307Leu missense_variant 0.12
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 0.37
PPE35 2170053 p.Thr187Ser missense_variant 0.35
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747437 p.Met54Ile missense_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
Rv3236c 3613240 c.-124G>A upstream_gene_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.14
rpoA 3878567 c.-60C>G upstream_gene_variant 0.4
clpC1 4039484 c.1221T>G synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242690 p.Val943Asp missense_variant 0.18
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4407934 p.Leu90Arg missense_variant 1.0