TB-Profiler result

Run: SRR6824364
Summary

Run ID: SRR6824364

Sample name:

Date: 20-10-2023 19:47:35

Number of reads: 13021226

Percentage reads mapped: 98.94

Strain: lineage4;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.His445Arg (0.95)
Isoniazid R katG c.-11435_*169del (0.95)
Ethambutol R embB p.Gln497Arg (0.96)
Pyrazinamide R pncA c.473delA (0.95)
Streptomycin R rrs n.517C>T (0.96)
Fluoroquinolones R gyrA p.Ala90Val (0.90)
Moxifloxacin R gyrA p.Ala90Val (0.90)
Ofloxacin R gyrA p.Ala90Val (0.90)
Levofloxacin R gyrA p.Ala90Val (0.90)
Ciprofloxacin R gyrA p.Ala90Val (0.90)
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 0.96
lineage4 Euro-American LAM;T;S;X;H None 0.05
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 7570 p.Ala90Val missense_variant 0.9 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Arg missense_variant 0.95 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.96 streptomycin
pncA 2288768 c.473delA frameshift_variant 0.95 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.96 ethambutol
katG 2153719 c.-11435_*169del transcript_ablation 0.95 isoniazid
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 0.98
mshA 575907 p.Ala187Val missense_variant 0.94
ccsA 620625 p.Ile245Met missense_variant 0.92
rpoB 760295 p.Asn163Lys missense_variant 0.95
rpoB 762909 p.Ile1035Val missense_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.93
mmpL5 776182 p.Asp767Asn missense_variant 0.93
mmpS5 779615 c.-710C>G upstream_gene_variant 0.95
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800657 c.-152G>T upstream_gene_variant 0.96
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 0.95
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726142 c.-51G>A upstream_gene_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612601 c.516C>T synonymous_variant 0.92
Rv3236c 3612813 p.Thr102Ala missense_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.96
aftB 4267647 p.Asp397Gly missense_variant 0.93
ethA 4326025 c.1449G>A synonymous_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.94
gid 4407927 p.Glu92Asp missense_variant 0.95