TB-Profiler result

Run: ERR4798868
Summary

Run ID: ERR4798868

Sample name:

Date: 20-10-2023 03:08:34

Number of reads: 4846392

Percentage reads mapped: 99.51

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.Ser450Leu (0.90)
Isoniazid R katG p.Ser315Thr (0.92)
Ethambutol R embB p.Met306Val (0.88), embB p.Gln853Pro (0.85)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.92)
Fluoroquinolones R gyrA p.Asp94Tyr (0.78)
Moxifloxacin R gyrA p.Asp94Tyr (0.78)
Ofloxacin R gyrA p.Asp94Tyr (0.78)
Levofloxacin R gyrA p.Asp94Tyr (0.78)
Ciprofloxacin R gyrA p.Asp94Tyr (0.78)
Aminoglycosides R rrs n.1401A>G (0.89)
Amikacin R rrs n.1401A>G (0.89)
Capreomycin R rrs n.1401A>G (0.89)
Kanamycin R rrs n.1401A>G (0.89)
Cycloserine
Ethionamide R ethA c.1047dupT (0.81), ethA c.1047dupT (0.81)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.81)
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 0.88
lineage4 Euro-American LAM;T;S;X;H None 0.05
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.9
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.9
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 0.78 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.9 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.92 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.89 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.92 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 0.81 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.88 ethambutol
embB 4249071 p.Gln853Pro missense_variant 0.85 ethambutol
ethA 4326426 c.1047dupT frameshift_variant 0.81 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 7283 c.-19G>T upstream_gene_variant 0.85
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.98
gyrA 9304 p.Gly668Asp missense_variant 0.96
fgd1 491742 c.960T>C synonymous_variant 0.93
mshA 575907 p.Ala187Val missense_variant 0.86
ccsA 620625 p.Ile245Met missense_variant 0.9
rpoC 762434 c.-936T>G upstream_gene_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
rpoC 764666 p.Gly433Ser missense_variant 0.76
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.97
mmpL5 776182 p.Asp767Asn missense_variant 0.89
mmpS5 779615 c.-710C>G upstream_gene_variant 0.87
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.87
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.89
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
pepQ 2860365 c.54G>T synonymous_variant 0.75
thyA 3074069 p.Val135Phe missense_variant 0.83
ald 3086788 c.-32T>C upstream_gene_variant 0.96
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
Rv3236c 3612813 p.Thr102Ala missense_variant 0.82
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 0.86
embA 4243460 c.228C>T synonymous_variant 0.92
embB 4249757 p.Thr1082Ala missense_variant 0.84
aftB 4267647 p.Asp397Gly missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.96
gid 4407927 p.Glu92Asp missense_variant 0.84