TB-Profiler result

Run: ERR4813371
Summary

Run ID: ERR4813371

Sample name:

Date: 20-10-2023 04:57:24

Number of reads: 4284155

Percentage reads mapped: 99.61

Strain: lineage4.3.2;lineage2.2.1

Drug-resistance: MDR-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.Gln432Pro (0.44)
Isoniazid R katG p.Ser315Thr (0.37)
Ethambutol
Pyrazinamide R pncA p.Thr160Pro (0.40)
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 0.6
lineage4.3 Euro-American (LAM) mainly-LAM None 0.44
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.61
lineage4.3.2 Euro-American (LAM) LAM3 None 0.42
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.59
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 761101 p.Gln432Pro missense_variant 0.44 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.37 isoniazid
pncA 2288764 p.Thr160Pro missense_variant 0.4 pyrazinamide
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 0.72
mshA 575907 p.Ala187Val missense_variant 0.68
ccsA 620625 p.Ile245Met missense_variant 0.56
rpoC 763031 c.-339T>C upstream_gene_variant 0.66
rpoC 764995 c.1626C>G synonymous_variant 0.32
rpoC 765926 p.Thr853Ala missense_variant 0.44
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.6
mmpL5 776182 p.Asp767Asn missense_variant 0.54
mmpS5 779615 c.-710C>G upstream_gene_variant 0.63
mmpS5 779630 c.-725T>C upstream_gene_variant 0.68
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.44
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.34
rpsA 1834177 c.636A>C synonymous_variant 0.53
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.62
PPE35 2167926 p.Leu896Ser missense_variant 0.71
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.46
thyA 3073868 p.Thr202Ala missense_variant 0.38
ald 3086788 c.-32T>C upstream_gene_variant 0.99
ald 3087755 c.936G>T synonymous_variant 0.63
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.5
clpC1 4038287 c.2418C>T synonymous_variant 0.53
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.44
aftB 4267647 p.Asp397Gly missense_variant 0.49
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.7
gid 4407721 p.Ala161Gly missense_variant 0.4
gid 4407927 p.Glu92Asp missense_variant 0.6
gid 4408050 p.Asn51Lys missense_variant 0.46
gid 4408156 p.Leu16Arg missense_variant 0.44