TB-Profiler result

Run: ERR229921

Summary

Run ID: ERR229921

Sample name:

Date: 19-10-2023 19:10:38

Number of reads: 5324607

Percentage reads mapped: 99.57

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 (0.98), rpoB p.Glu761Asp (0.99)
Isoniazid R katG p.Ser315Thr (0.99)
Ethambutol R embB p.Asp354Ala (0.98)
Pyrazinamide
Streptomycin R rrs n.517C>T (0.98)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-37G>T (1.00)
Cycloserine
Ethionamide R ethA c.-7T>C (0.94)
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 0.97
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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 0.98 rifampicin
rpoB 762089 p.Glu761Asp missense_variant 0.99 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
embB 4247574 p.Asp354Ala missense_variant 0.98 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 0.94 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 0.98
mshA 575907 p.Ala187Val missense_variant 0.95
ccsA 620625 p.Ile245Met missense_variant 0.98
rpoB 759930 p.Leu42Phe missense_variant 0.97
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 0.97
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.99
mmpS5 779615 c.-710C>G upstream_gene_variant 0.99
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 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289226 p.Ile6Leu missense_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448544 p.Leu14Arg missense_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.98
aftB 4267647 p.Asp397Gly missense_variant 0.99
whiB6 4338563 c.-42G>T upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.98
gid 4407927 p.Glu92Asp missense_variant 0.97