TB-Profiler result

Run: ERR4796816

Summary

Run ID: ERR4796816

Sample name:

Date: 20-10-2023 02:01:08

Number of reads: 6203852

Percentage reads mapped: 99.64

Strain: lineage2.2.1.1

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 (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.58), embB p.Gly406Ser (0.33)
Pyrazinamide R pncA p.Val139Ala (0.49), pncA c.-11A>G (0.36)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrB p.Glu501Asp (0.57), gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrB p.Glu501Asp (0.57), gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrB p.Glu501Asp (0.57), gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrB p.Glu501Asp (0.57), gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrB p.Glu501Asp (0.57), gyrA p.Asp94Gly (1.00)
Aminoglycosides R rrs n.1401A>G (0.51)
Amikacin R rrs n.1401A>G (0.51)
Capreomycin R rrs n.1401A>G (0.51)
Kanamycin R rrs n.1401A>G (0.51)
Cycloserine
Ethionamide R ethA c.754_755dupGC (0.55), ethA c.754_755dupGC (0.55)
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 1.0
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.62
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
gyrB 6742 p.Glu501Asp missense_variant 0.57 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.51 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Ala missense_variant 0.49 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.36 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.58 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.33 ethambutol
ethA 4326718 c.754_755dupGC frameshift_variant 0.55 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 7362 p.Glu21Gln missense_variant 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.37
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764363 p.Gly332Ser missense_variant 0.74
rpoC 764666 p.Gly433Ser missense_variant 0.45
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
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 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
eis 2714846 p.Val163Ile missense_variant 0.61
ald 3086788 c.-32T>C upstream_gene_variant 0.35
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4241022 p.Ala387Val missense_variant 0.39
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247880 p.Val456Ala missense_variant 0.65
embB 4248115 c.1602C>T synonymous_variant 0.57
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327322 p.Pro51His missense_variant 0.38
whiB6 4338410 p.Pro38Ala missense_variant 0.62
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.47
gid 4407927 p.Glu92Asp missense_variant 0.99
gid 4408385 c.-183C>T upstream_gene_variant 0.46