TB-Profiler result

Run: SRR6832769
Summary

Run ID: SRR6832769

Sample name:

Date: 04-04-2023 17:38:05

Number of reads: 2037877

Percentage reads mapped: 99.59

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 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
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 2289207 p.Asp12Ala missense_variant 1.0 pyrazinamide
embB 4247469 p.Tyr319Cys missense_variant 1.0 ethambutol
ethA 4327054 p.Tyr140* stop_gained 1.0 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
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 491238 c.456C>T synonymous_variant 0.11
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
rpoB 761234 c.1428G>A synonymous_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766744 p.Gln1125His 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 1.0
mmpR5 779359 p.Ala124Ser missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801132 c.324T>C synonymous_variant 0.1
Rv1258c 1406742 p.His200Arg missense_variant 0.11
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168603 c.2010C>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064630 p.Ala521Asp missense_variant 0.1
thyX 3067540 p.Ala136Thr missense_variant 0.15
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612626 p.Ala164Val missense_variant 0.83
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4039358 p.Ser449Arg missense_variant 0.12
embC 4239899 p.Arg13Trp missense_variant 0.1
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 4243963 p.Val244Ala missense_variant 0.1
embA 4244350 p.Leu373Pro missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
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 4407927 p.Glu92Asp missense_variant 1.0