TB-Profiler result

Run: SRR11972272

Summary

Run ID: SRR11972272

Sample name:

Date: 03-04-2023 05:34:23

Number of reads: 575127

Percentage reads mapped: 98.08

Strain: lineage2.2.1.1

Drug-resistance: RR-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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.07
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 761166 p.Pro454Ser missense_variant 0.4 rifampicin
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 5716 c.477G>A synonymous_variant 0.17
gyrA 6490 c.-812T>A upstream_gene_variant 0.5
gyrB 6558 p.Gly440Asp missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7740 p.Glu147* stop_gained 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.77
ccsA 620625 p.Ile245Met missense_variant 0.48
rpoB 762319 p.Ser838Tyr missense_variant 0.2
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 0.5
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406145 p.Ala399Val missense_variant 0.47
Rv1258c 1406760 c.580_581insC frameshift_variant 0.33
Rv1258c 1406815 p.Ile176Val missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
rpsA 1834080 p.Arg180His missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101663 c.1380G>A synonymous_variant 0.25
ndh 2102172 c.870dupC frameshift_variant 0.11
ndh 2103225 c.-183A>C upstream_gene_variant 0.29
katG 2153979 p.Tyr711* stop_gained 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155017 c.1095G>A synonymous_variant 0.12
katG 2155253 p.Glu287Lys missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168211 p.Ile801Asn missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223321 c.-157G>C upstream_gene_variant 0.12
eis 2714846 p.Val163Ile missense_variant 0.32
folC 2746534 p.Asn355Lys missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448611 c.108A>G synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613058 p.Val20Ala missense_variant 0.11
Rv3236c 3613160 c.-44C>T upstream_gene_variant 0.18
fbiA 3640645 p.Ser35Pro missense_variant 0.12
alr 3840651 p.Val257Ala missense_variant 0.11
alr 3841258 p.His55Asn missense_variant 0.15
clpC1 4039161 p.His515Gly missense_variant 0.11
clpC1 4039169 p.Glu512Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244507 c.1275G>T synonymous_variant 0.24
embB 4248115 c.1602C>T synonymous_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
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