TB-Profiler result

Run: SRR22175250

Summary

Run ID: SRR22175250

Sample name:

Date: 04-04-2023 04:02:52

Number of reads: 77275

Percentage reads mapped: 99.42

Strain: lineage2.2.1

Drug-resistance: HR-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 0.11
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.18
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.1
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
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
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
folC 2747471 p.Ile43Thr missense_variant 1.0 para-aminosalicylic_acid
alr 3840393 p.Met343Thr missense_variant 1.0 cycloserine
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4327304 p.Ser57Tyr missense_variant 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 1.0
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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764533 c.1164C>A synonymous_variant 1.0
rpoC 766646 p.Asp1093Tyr missense_variant 0.4
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 779060 p.Gly24Val missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303502 p.Leu191Pro missense_variant 0.5
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416493 c.855C>G synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101767 p.Arg426Ser missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2168505 p.Gly703Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3074221 p.Ala84Val missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4241022 p.Ala387Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243368 p.Pro46Ser missense_variant 0.4
embA 4243460 c.228C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0