TB-Profiler result

Run: SRR5709748

Summary

Run ID: SRR5709748

Sample name:

Date: 20-10-2023 16:38:04

Number of reads: 2262753

Percentage reads mapped: 99.69

Strain: lineage2.1

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.Gln432Pro (0.98), rpoC p.Gly332Arg (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Trp119Arg (0.83), pncA p.Gly105Asp (0.19)
Streptomycin R gid c.386delG (0.14), gid c.351delG (0.85)
Fluoroquinolones R gyrA p.Ser91Pro (0.21), gyrA p.Asp94His (0.77)
Moxifloxacin R gyrA p.Ser91Pro (0.21), gyrA p.Asp94His (0.77)
Ofloxacin R gyrA p.Ser91Pro (0.21), gyrA p.Asp94His (0.77)
Levofloxacin R gyrA p.Ser91Pro (0.21), gyrA p.Asp94His (0.77)
Ciprofloxacin R gyrA p.Ser91Pro (0.21), gyrA p.Asp94His (0.77)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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
lineage2.1 East-Asian (non-Beijing) None None 1.0
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 7572 p.Ser91Pro missense_variant 0.21 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94His missense_variant 0.77 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761101 p.Gln432Pro missense_variant 0.98 rifampicin
rpoC 764363 p.Gly332Arg missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288887 p.Trp119Arg missense_variant 0.83 pyrazinamide
pncA 2288928 p.Gly105Asp missense_variant 0.19 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4407816 c.386delG frameshift_variant 0.14 streptomycin
gid 4407851 c.351delG frameshift_variant 0.85 streptomycin
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
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303162 p.Pro78Ser missense_variant 1.0
fbiC 1304443 p.Ala505Thr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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
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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246088 c.-426A>G upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0