TB-Profiler result

Run: SRR3085264

Summary

Run ID: SRR3085264

Sample name:

Date: 04-04-2023 04:56:05

Number of reads: 1953998

Percentage reads mapped: 99.36

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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289057 p.Pro62Leu missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.9 ethambutol
ethA 4327363 c.110delA frameshift_variant 1.0 ethionamide, 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 5176 c.-63_-62delGT upstream_gene_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9543 p.Lys748Glu missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620697 c.807C>T synonymous_variant 0.12
ccsA 620843 p.His318Arg missense_variant 0.11
rpoB 762250 p.Leu815Pro missense_variant 0.12
rpoB 762880 p.Met1025Thr missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764703 p.Lys445Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775847 c.2634G>T synonymous_variant 0.4
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 778480 c.1A>G start_lost 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800794 c.-15A>G upstream_gene_variant 0.11
fbiC 1304826 c.1900delT frameshift_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407145 p.Val66Ile missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674901 p.Asp234Asn missense_variant 0.12
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 2156204 c.-93A>T upstream_gene_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168088 p.Pro842Leu missense_variant 0.11
PPE35 2169625 p.Gly330Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519315 p.Ser401Thr missense_variant 0.12
eis 2715290 p.Gly15Trp missense_variant 0.11
eis 2715362 c.-30T>C upstream_gene_variant 0.12
folC 2746198 c.1401C>G synonymous_variant 0.12
folC 2747383 c.216C>T synonymous_variant 0.15
folC 2747513 p.Gln29Arg missense_variant 0.12
pepQ 2859755 p.Phe222Ile missense_variant 0.12
pepQ 2860205 p.Glu72* stop_gained 0.1
Rv2752c 3064605 c.1587C>A synonymous_variant 0.14
thyA 3073962 c.510G>A synonymous_variant 0.11
thyA 3074605 c.-134T>G upstream_gene_variant 0.17
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448555 p.Gly18Arg missense_variant 0.12
Rv3083 3448819 p.Thr106Ala missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841429 c.-9T>C upstream_gene_variant 0.1
clpC1 4038701 c.2004G>A synonymous_variant 0.11
clpC1 4039661 c.1043dupG frameshift_variant 0.11
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 1.0
embA 4244159 c.927G>T synonymous_variant 0.4
embA 4245681 p.Gly817Ser missense_variant 0.12
embA 4246437 p.Ala1069Thr missense_variant 0.11
embB 4248799 c.2286T>C synonymous_variant 0.17
aftB 4267528 p.Ala437Ser missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267742 c.1095G>A synonymous_variant 0.12
ethA 4328358 c.-885C>T upstream_gene_variant 0.11
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407790 p.Ala138Val missense_variant 0.11
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408186 p.Pro6Leu missense_variant 0.18