TB-Profiler result

Run: SRR25389507
Summary

Run ID: SRR25389507

Sample name:

Date: 13-02-2024 08:52:36

Number of reads: 13802679

Percentage reads mapped: 99.41

Strain: lineage2.2.2;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.His445Tyr (0.18), rpoB p.Ser450Leu (0.84)
Isoniazid R katG p.Ser315Thr (0.21)
Ethambutol
Pyrazinamide
Streptomycin R gid p.Leu79Ser (0.20)
Fluoroquinolones R gyrA p.Asp94Tyr (0.18)
Moxifloxacin R gyrA p.Asp94Tyr (0.18)
Ofloxacin R gyrA p.Asp94Tyr (0.18)
Levofloxacin R gyrA p.Asp94Tyr (0.18)
Ciprofloxacin R gyrA p.Asp94Tyr (0.18)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.110delA (0.18), ethA c.110delA (0.18)
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 0.8
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.17
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 7581 p.Asp94Tyr missense_variant 0.18 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 0.18 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.84 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.21 isoniazid
ethA 4327363 c.110delA frameshift_variant 0.18 ethionamide, ethionamide
gid 4407967 p.Leu79Ser missense_variant 0.2 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
mshA 575907 p.Ala187Val missense_variant 0.82
ccsA 620625 p.Ile245Met missense_variant 0.84
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.78
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475225 n.1568A>C non_coding_transcript_exon_variant 0.24
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918317 c.378T>G synonymous_variant 0.15
katG 2154629 p.Gly495Cys missense_variant 0.82
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156027 p.Pro29Ser missense_variant 0.8
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064850 p.Phe448Leu missense_variant 0.85
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 1.0
alr 3841338 p.Ile28Thr missense_variant 0.17
panD 4044086 p.Ser66Gly missense_variant 0.82
embC 4241791 c.1929G>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
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
gid 4407927 p.Glu92Asp missense_variant 1.0