TB-Profiler result

Run: SRR23311000
Summary

Run ID: SRR23311000

Sample name:

Date: 14-03-2023 06:18:33

Number of reads: 3516683

Percentage reads mapped: 99.58

Strain: lineage2.2

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 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
mmpR5 779181 c.198dupG frameshift_variant 0.14 clofazimine, bedaquiline
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
tlyA 1918350 c.413dupG frameshift_variant 0.82 capreomycin
tlyA 1918350 c.412_413dupGG frameshift_variant 0.73 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288954 p.Lys96Asn missense_variant 0.98 pyrazinamide
embB 4248002 p.Gln497Lys missense_variant 0.98 ethambutol
ethA 4327292 p.Thr61Met missense_variant 0.98 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 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 0.99
mshA 575907 p.Ala187Val missense_variant 0.99
mshA 576613 c.1266A>C synonymous_variant 0.29
mshA 576616 c.1269G>C synonymous_variant 0.16
ccsA 620625 p.Ile245Met missense_variant 0.96
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 766645 p.Glu1092Asp missense_variant 0.99
rpoC 767123 p.Val1252Leu missense_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.99
mmpR5 779392 p.Arg135Trp missense_variant 0.28
mmpR5 779412 c.424dupC frameshift_variant 0.12
mmpR5 779450 c.465delG frameshift_variant 0.3
mmpS5 779615 c.-710C>G upstream_gene_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
fabG1 1673553 p.Asp38Glu missense_variant 0.26
rpsA 1834177 c.636A>C synonymous_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.58
fbiD 3339746 p.Ala210Gly missense_variant 0.25
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.19
Rv3236c 3612813 p.Thr102Ala missense_variant 0.96
rpoA 3878641 c.-134C>G upstream_gene_variant 0.62
embC 4240409 p.Pro183Ala missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.98
embB 4246527 p.Ala5Gly missense_variant 0.28
embB 4246584 p.Arg24Pro missense_variant 0.19
aftB 4267646 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 0.99