TB-Profiler result

Run: ERR4830155

Summary

Run ID: ERR4830155

Sample name:

Date: 20-10-2023 01:34:26

Number of reads: 3511138

Percentage reads mapped: 99.59

Strain: lineage2.2.1

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 (0.97)
Isoniazid R katG p.Ser315Thr (0.98)
Ethambutol R embB p.Gln497Arg (0.97)
Pyrazinamide R pncA p.Gln10Lys (0.95)
Streptomycin R rpsL p.Lys43Arg (0.97)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (0.98)
Cycloserine
Ethionamide R ethA c.83_84delCG (0.97), ethA c.83_84delCG (0.97)
Clofazimine
Para-aminosalicylic_acid R folC p.Glu40Gly (0.99)
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 0.97
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.98
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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 0.97 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.97 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289214 p.Gln10Lys missense_variant 0.95 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.98 kanamycin
folC 2747480 p.Glu40Gly missense_variant 0.99 para-aminosalicylic_acid
embB 4248003 p.Gln497Arg missense_variant 0.97 ethambutol
ethA 4327389 c.83_84delCG frameshift_variant 0.97 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.99
mshA 575907 p.Ala187Val missense_variant 0.97
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
rpoC 764918 p.Val517Leu missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.99
mmpS5 779615 c.-710C>G upstream_gene_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.99
embA 4243460 c.228C>T synonymous_variant 0.96
aftB 4267647 p.Asp397Gly missense_variant 0.94
whiB6 4338371 p.Thr51Pro missense_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.94
gid 4407927 p.Glu92Asp missense_variant 0.98