TB-Profiler result

Run: ERR4799344

Summary

Run ID: ERR4799344

Sample name:

Date: 20-10-2023 03:34:12

Number of reads: 3483885

Percentage reads mapped: 99.64

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.Ser450Leu (0.96)
Isoniazid R fabG1 c.-8T>C (0.82), katG p.Ser315Thr (0.96)
Ethambutol R embB p.Met306Val (0.94)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.97)
Fluoroquinolones R gyrA p.Asp94Gly (0.94)
Moxifloxacin R gyrA p.Asp94Gly (0.94)
Ofloxacin R gyrA p.Asp94Gly (0.94)
Levofloxacin R gyrA p.Asp94Gly (0.94)
Ciprofloxacin R gyrA p.Asp94Gly (0.94)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-8T>C (0.82), ethA c.1371_1381delGAATCAGAACT (0.90), ethA c.1371_1381delGAATCAGAACT (0.90)
Clofazimine
Para-aminosalicylic_acid R folC p.Ser150Gly (0.83)
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 0.95
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.95
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.96
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 7582 p.Asp94Gly missense_variant 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.96 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.97 streptomycin
fabG1 1673432 c.-8T>C upstream_gene_variant 0.82 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.96 isoniazid
folC 2747151 p.Ser150Gly missense_variant 0.83 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.94 ethambutol
ethA 4326092 c.1371_1381delGAATCAGAACT frameshift_variant 0.9 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.96
ccsA 620625 p.Ile245Met missense_variant 0.93
rpoB 762477 p.Lys891Glu missense_variant 0.9
rpoC 763031 c.-339T>C upstream_gene_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 0.93
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 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.93
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
Rv1979c 2223293 c.-129A>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 3612813 p.Thr102Ala missense_variant 0.92
embC 4241022 p.Ala387Val missense_variant 0.87
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.93
aftB 4267647 p.Asp397Gly missense_variant 0.97
ubiA 4269309 p.Trp175Cys missense_variant 0.82
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.92
gid 4407927 p.Glu92Asp missense_variant 0.99