TB-Profiler result

Run: SRR11972192
Summary

Run ID: SRR11972192

Sample name:

Date: 03-04-2023 05:31:25

Number of reads: 198122

Percentage reads mapped: 99.1

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4326250 p.Tyr408* stop_gained 0.18 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
gyrB 5791 c.552A>G synonymous_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7454 c.153G>A synonymous_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9301 p.Ala667Asp missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491635 p.Ile285Val missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491758 p.Ser326Pro missense_variant 0.25
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620166 c.276G>A synonymous_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759624 c.-183G>A upstream_gene_variant 0.13
rpoB 760341 p.Val179Met missense_variant 0.12
rpoB 762913 p.His1036Arg missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765942 p.Lys858Arg missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777462 p.Ala340Val missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781622 c.63C>G synonymous_variant 0.5
rplC 801238 p.Val144Met missense_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461098 c.54C>T synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473001 n.1156G>A non_coding_transcript_exon_variant 0.29
fabG1 1673609 p.Gly57Asp missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168320 p.Thr765Ser missense_variant 0.22
PPE35 2169638 c.975T>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289799 c.-558G>A upstream_gene_variant 0.18
pncA 2289889 c.-648C>A upstream_gene_variant 0.2
kasA 2518794 p.Ser227Cys missense_variant 0.17
eis 2714190 c.1143G>A synonymous_variant 0.2
eis 2714427 c.906G>A synonymous_variant 0.14
eis 2714635 p.Leu233His missense_variant 0.15
eis 2714846 p.Val163Ile missense_variant 1.0
folC 2747725 c.-127C>T upstream_gene_variant 0.18
pepQ 2860404 c.15G>A synonymous_variant 0.29
thyA 3073896 c.576C>A synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448578 c.75C>T synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475252 p.Lys416* stop_gained 0.25
whiB7 3568610 p.Asp24Asn missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641153 p.Ala204Val missense_variant 0.67
alr 3841546 c.-126C>A upstream_gene_variant 0.15
rpoA 3878041 p.Gly156Asp missense_variant 0.15
clpC1 4038563 p.Asp714Glu missense_variant 0.12
clpC1 4039982 c.723G>A synonymous_variant 0.4
clpC1 4040362 p.Glu115Lys missense_variant 0.17
clpC1 4040870 c.-166T>A upstream_gene_variant 0.22
embC 4239887 p.Arg9Cys missense_variant 0.33
embC 4239936 p.Asn25Ser missense_variant 0.4
embC 4240655 p.Ala265Thr missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246372 p.Arg1047His missense_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269736 p.Leu33Pro missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407600 c.603C>A synonymous_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408187 p.Pro6Ala missense_variant 0.22