TB-Profiler result

Run: ERR4798248

Summary

Run ID: ERR4798248

Sample name:

Date: 20-10-2023 02:51:28

Number of reads: 6781526

Percentage reads mapped: 99.61

Strain: lineage2.2.1.1

Drug-resistance: MDR-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 fabG1 c.-8T>C (0.47), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Thr177Pro (0.41), pncA c.-11A>G (0.60)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1484G>T (0.50)
Amikacin R rrs n.1484G>T (0.50)
Capreomycin R rrs n.1484G>T (0.50)
Kanamycin R rrs n.1484G>T (0.50)
Cycloserine
Ethionamide R fabG1 c.-8T>C (0.47), ethA c.578dupC (0.54), ethA c.578dupC (0.54)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.45)
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.47)
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 0.55
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.47 linezolid
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.5 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>C upstream_gene_variant 0.47 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288713 p.Thr177Pro missense_variant 0.41 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.6 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.45 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326895 c.578dupC frameshift_variant 0.54 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 1.0
gyrA 7581 p.Asp94Cys missense_variant 0.45
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 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764363 p.Gly332Ser missense_variant 0.57
rpoC 764840 p.Ile491Val missense_variant 0.42
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779130 c.144dupC frameshift_variant 0.43
mmpR5 779239 p.Ala84Thr missense_variant 0.56
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
rrl 1475951 n.2294G>A non_coding_transcript_exon_variant 0.52
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101844 p.His400Arg missense_variant 0.64
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 0.55
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087692 c.874dupG frameshift_variant 0.42
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4241022 p.Ala387Val missense_variant 0.45
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 0.53
embB 4248115 c.1602C>T synonymous_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326296 p.Leu393Arg missense_variant 0.4
whiB6 4338591 c.-70G>C upstream_gene_variant 0.65
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.42
gid 4407927 p.Glu92Asp missense_variant 1.0