TB-Profiler result

Run: SRR8651658
Summary

Run ID: SRR8651658

Sample name:

Date: 21-10-2023 13:00:29

Number of reads: 4215296

Percentage reads mapped: 99.41

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Gln432Leu (0.96)
Isoniazid R fabG1 c.-17G>T (0.98), katG p.Val710Ala (0.25)
Ethambutol R embB p.Gly406Cys (0.98)
Pyrazinamide R pncA c.-11A>G (0.98)
Streptomycin R rpsL p.Lys88Arg (0.98)
Fluoroquinolones R gyrA p.Ala90Val (0.99)
Moxifloxacin R gyrA p.Ala90Val (0.99)
Ofloxacin R gyrA p.Ala90Val (0.99)
Levofloxacin R gyrA p.Ala90Val (0.99)
Ciprofloxacin R gyrA p.Ala90Val (0.99)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-17G>T (0.98)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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
gyrA 7570 p.Ala90Val missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761101 p.Gln432Leu missense_variant 0.96 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.98 streptomycin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.98 isoniazid, ethionamide
katG 2153983 p.Val710Ala missense_variant 0.25 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.98 pyrazinamide
embB 4247729 p.Gly406Cys missense_variant 0.98 ethambutol
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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.99
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoB 761533 p.Ser576Leu missense_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 764942 p.His525Asn missense_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155691 p.Leu141Val missense_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726121 c.-72C>T upstream_gene_variant 0.94
pepQ 2860181 p.Gly80Arg missense_variant 1.0
Rv2752c 3067172 c.-981A>G upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448913 p.Ile137Thr missense_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640492 c.-51G>A upstream_gene_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327065 p.Cys137Arg missense_variant 0.99
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