TB-Profiler result

Run: ERR7911579
Summary

Run ID: ERR7911579

Sample name:

Date: 19-10-2023 13:29:04

Number of reads: 4182892

Percentage reads mapped: 99.62

Strain: lineage4.3.3;lineage2.2.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.73)
Isoniazid R fabG1 c.-15C>T (0.62), katG p.Ser315Thr (0.55)
Ethambutol R embB p.Met306Ile (0.69)
Pyrazinamide R pncA p.Thr160Ala (0.62), pncA p.Thr100Ile (0.56)
Streptomycin R rrs n.514A>C (0.73)
Fluoroquinolones R gyrA p.Ala90Val (0.68)
Moxifloxacin R gyrA p.Ala90Val (0.68)
Ofloxacin R gyrA p.Ala90Val (0.68)
Levofloxacin R gyrA p.Ala90Val (0.68)
Ciprofloxacin R gyrA p.Ala90Val (0.68)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.62)
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 0.66
lineage4 Euro-American LAM;T;S;X;H None 0.34
lineage4.3 Euro-American (LAM) mainly-LAM None 0.37
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.66
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.65
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.36
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
gyrA 7570 p.Ala90Val missense_variant 0.68 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.73 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.73 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.62 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.55 isoniazid
pncA 2288764 p.Thr160Ala missense_variant 0.62 pyrazinamide
pncA 2288943 p.Thr100Ile missense_variant 0.56 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.69 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
gyrB 6507 p.Ala423Val missense_variant 0.42
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.43
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491328 c.546C>G synonymous_variant 0.68
fgd1 491330 p.Lys183Met missense_variant 0.69
fgd1 491742 c.960T>C synonymous_variant 0.67
mshA 575907 p.Ala187Val missense_variant 0.69
ccsA 620625 p.Ile245Met missense_variant 0.63
rpoC 763031 c.-339T>C upstream_gene_variant 0.61
rpoC 764822 p.Asp485Tyr missense_variant 0.61
rpoC 764995 c.1626C>G synonymous_variant 0.38
mmpL5 775592 c.2889G>A synonymous_variant 0.71
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 0.55
mmpL5 776182 p.Asp767Asn missense_variant 0.56
mmpS5 779615 c.-710C>G upstream_gene_variant 0.64
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406359 p.Ile328Val missense_variant 0.72
Rv1258c 1406760 c.580_581insC frameshift_variant 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.31
rpsA 1834177 c.636A>C synonymous_variant 0.61
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.73
PPE35 2167926 p.Leu896Ser missense_variant 0.7
Rv1979c 2223051 p.Glu38Asp missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.26
Rv2752c 3065824 p.Pro123Leu missense_variant 0.36
thyA 3073868 p.Thr202Ala missense_variant 0.37
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449315 p.Trp271* stop_gained 0.65
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.65
clpC1 4038287 c.2418C>T synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.66
aftB 4267647 p.Asp397Gly missense_variant 0.66
whiB6 4338365 p.Cys53Arg missense_variant 0.6
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.64
gid 4407927 p.Glu92Asp missense_variant 0.71
gid 4408156 p.Leu16Arg missense_variant 0.34