TB-Profiler result

Run: SRR671839

Summary

Run ID: SRR671839

Sample name:

Date: 20-10-2023 21:49:49

Number of reads: 5711739

Percentage reads mapped: 99.48

Strain: 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.His445Tyr (1.00)
Isoniazid R fabG1 c.-8T>A (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-16C>T (0.98), embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Cys72Arg (1.00)
Streptomycin R rpsL p.Lys43Arg (0.99)
Fluoroquinolones R gyrA p.Ala90Val (0.99)
Moxifloxacin R gyrA p.Ala90Val (0.99)
Ofloxacin R gyrA p.Ala90Val (0.99)
Levofloxacin R gyrA p.Ala90Val (0.99)
Ciprofloxacin R gyrA p.Ala90Val (0.99)
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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289028 p.Cys72Arg missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.98 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 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 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761005 p.Thr400Ile missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766131 p.Tyr921Cys missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779048 p.Val20Ala missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290039 c.-798C>A upstream_gene_variant 1.0
thyX 3067954 c.-9G>A upstream_gene_variant 1.0
thyA 3073948 p.Pro175Gln missense_variant 1.0
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 1.0
fbiA 3640346 c.-197G>A upstream_gene_variant 1.0
fbiA 3640377 c.-166G>A upstream_gene_variant 1.0
clpC1 4038517 p.Met730Val missense_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338593 c.-73delT upstream_gene_variant 1.0
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0