TB-Profiler result

Run: ERR4809240

Summary

Run ID: ERR4809240

Sample name:

Date: 20-10-2023 14:36:27

Number of reads: 3306175

Percentage reads mapped: 99.6

Strain: lineage4.2.1;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.Leu430Pro (0.20), rpoB p.Ser450Leu (0.31)
Isoniazid R katG p.Ser315Thr (0.57)
Ethambutol R embB p.Met306Val (0.14)
Pyrazinamide R pncA c.-7T>C (0.18)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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 0.49
lineage4 Euro-American LAM;T;S;X;H None 0.49
lineage4.2 Euro-American H;T;LAM None 0.51
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.53
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.53
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.52
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 761095 p.Leu430Pro missense_variant 0.2 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.31 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.57 isoniazid
pncA 2289248 c.-7T>C upstream_gene_variant 0.18 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.14 ethambutol
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 0.99
fgd1 491238 c.456C>T synonymous_variant 0.41
fgd1 491247 c.465C>T synonymous_variant 0.44
fgd1 491742 c.960T>C synonymous_variant 0.6
mshA 575907 p.Ala187Val missense_variant 0.53
ccsA 620625 p.Ile245Met missense_variant 0.43
rpoC 763031 c.-339T>C upstream_gene_variant 0.62
rpoC 764123 p.Phe252Leu missense_variant 0.42
rpoC 764817 p.Val483Ala missense_variant 0.26
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.58
mmpL5 776182 p.Asp767Asn missense_variant 0.57
mmpS5 779615 c.-710C>G upstream_gene_variant 0.49
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.52
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.45
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.43
PPE35 2167926 p.Leu896Ser missense_variant 0.41
PPE35 2169879 p.Phe245Cys missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518773 p.Asn220Ser missense_variant 0.49
ald 3086742 c.-78A>C upstream_gene_variant 0.41
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.57
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243218 c.-15C>G upstream_gene_variant 0.34
embA 4243460 c.228C>T synonymous_variant 0.45
embB 4249594 c.3081G>A synonymous_variant 0.53
aftB 4267647 p.Asp397Gly missense_variant 0.42
ethA 4328376 c.-903G>C upstream_gene_variant 0.55
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.48
gid 4407620 p.Tyr195His missense_variant 0.49
gid 4407927 p.Glu92Asp missense_variant 0.52