TB-Profiler result

Run: SRR8651598
Summary

Run ID: SRR8651598

Sample name:

Date: 21-10-2023 13:01:36

Number of reads: 6103786

Percentage reads mapped: 98.07

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.Leu430Pro (0.94), rpoB p.His445Asn (0.91)
Isoniazid R fabG1 c.-15C>T (0.98), katG p.Ser315Thr (0.53)
Ethambutol
Pyrazinamide R pncA c.393dupC (0.24), pncA c.393dupC (0.24)
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (0.96)
Moxifloxacin R gyrA p.Ala90Val (0.96)
Ofloxacin R gyrA p.Ala90Val (0.96)
Levofloxacin R gyrA p.Ala90Val (0.96)
Ciprofloxacin R gyrA p.Ala90Val (0.96)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
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 0.96 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 0.94 rifampicin
rpoB 761139 p.His445Asn missense_variant 0.91 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.98 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.53 isoniazid
pncA 2288848 c.393dupC frameshift_variant 0.24 pyrazinamide, pyrazinamide
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 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.96
mmpL5 777745 p.Gly246Ser missense_variant 0.93
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 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.83
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2168712 p.Ala634Val missense_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>C upstream_gene_variant 0.86
embA 4243460 c.228C>T synonymous_variant 0.99
embA 4244055 p.Gly275Ser missense_variant 0.89
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338594 c.-73T>G upstream_gene_variant 0.93
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407927 p.Glu92Asp missense_variant 0.99