TB-Profiler result

Run: SRR23310845
Summary

Run ID: SRR23310845

Sample name:

Date: 14-03-2023 00:08:37

Number of reads: 1671695

Percentage reads mapped: 99.59

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
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 2289009 p.Gly78Asp missense_variant 1.0 pyrazinamide
folC 2747141 p.Glu153Ala missense_variant 0.88 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326463 c.1010delT frameshift_variant 0.97 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.98
mshA 575907 p.Ala187Val missense_variant 0.98
mshA 576113 p.Arg256Gly missense_variant 0.16
mshA 576456 p.Val370Gly missense_variant 0.24
mshA 576613 c.1266A>C synonymous_variant 0.23
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762285 p.Arg827Cys missense_variant 0.96
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.19
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
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 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.28
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 2170065 p.Ala183Gly missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.12
ribD 2986827 c.-12G>A upstream_gene_variant 0.16
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.71
fbiD 3339749 p.Val211Gly missense_variant 0.6
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>C synonymous_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878597 c.-90G>C upstream_gene_variant 0.44
rpoA 3878641 c.-134C>G upstream_gene_variant 0.82
embC 4240409 p.Pro183Ala missense_variant 0.37
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.96
embA 4243460 c.228C>T synonymous_variant 0.96
embB 4246527 p.Ala5Gly missense_variant 0.21
embB 4246529 p.Ser6Arg missense_variant 0.29
embB 4246584 p.Arg24Pro missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.96
gid 4407927 p.Glu92Asp missense_variant 1.0