TB-Profiler result

Run: SRR5152916
Summary

Run ID: SRR5152916

Sample name:

Date: 2024-10-04T19:40:59.192784

Number of reads: 7216365

Percentage reads mapped: 99.45

Median coverage: 135.0

Strain: lineage4.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.22
lineage4.2 Euro-American None 0.77
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.76
lineage4.3.3 Euro-American (LAM) RD115 0.22
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Tyr Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Asn Assoc w R High-level resistance
c.-10A>C Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
rpoB 761139 p.His445Tyr missense_variant 0.84 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.26 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.81 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Asn missense_variant 0.27 isoniazid Assoc w R High-level resistance
katG 2156121 c.-10A>C upstream_gene_variant 0.83 isoniazid Uncertain significance Mutation from literature
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 Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.27 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.18 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.73 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.27 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.76 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.82 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.24 isoniazid Not assoc w R
katG 2156354 c.-243G>A upstream_gene_variant 0.8 isoniazid Uncertain significance
PPE35 2169879 p.Phe245Cys missense_variant 0.66 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2517966 c.-149G>A upstream_gene_variant 0.84 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.23 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.27 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.25 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.75 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.23 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.77 ethambutol Not assoc w R - Interim
aftB 4268137 c.700C>T synonymous_variant 0.79 ethambutol Not assoc w R - Interim
ethA 4328376 c.-903G>C upstream_gene_variant 0.73 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.99 kanamycin
capreomycin
amikacin
gid 4407955 p.Arg83Pro missense_variant 0.78 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.25 streptomycin Not assoc w R