TB-Profiler result

Run: SRR28394232
Summary

Run ID: SRR28394232

Sample name:

Date: 2024-05-22T13:24:40.373785

Number of reads: 4456599

Percentage reads mapped: 99.71

Median coverage: 130.0

Strain: lineage4

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
pyrazinamide pncA p.Ile133Thr Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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 761155 p.Ser450Leu missense_variant 0.99 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288844 p.Ile133Thr missense_variant 1.0 pyrazinamide Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 0.98 ethambutol 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575837 c.490C>T synonymous_variant 0.98 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rpoB 761889 p.Val695Leu missense_variant 1.0 rifampicin Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777875 c.605delG frameshift_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpR5 779181 c.198dupG frameshift_variant 0.99 clofazimine Assoc w R
bedaquiline Assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.99 linezolid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.98 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2101831 c.1212G>A synonymous_variant 0.99 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
katG 2156173 c.-62C>A upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726141 c.-52C>A upstream_gene_variant 0.97 isoniazid Uncertain significance
Rv2752c 3065517 c.675C>T synonymous_variant 0.99 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
thyA 3074495 c.-24C>T upstream_gene_variant 0.99 para-aminosalicylic_acid
Rv3236c 3612219 p.Val300Ile missense_variant 1.0 pyrazinamide Uncertain significance
rpoA 3878595 c.-88C>T upstream_gene_variant 0.24 rifampicin
rpoA 3878635 c.-128C>T upstream_gene_variant 0.31 rifampicin
glpK 4138812 p.Pro315Leu missense_variant 0.18 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4243017 p.Asp1052Ala missense_variant 0.96 ethambutol Uncertain significance
embB 4246734 p.Leu74Pro missense_variant 1.0 ethambutol Uncertain significance
ethA 4326927 p.Ser183Arg missense_variant 0.15 ethionamide Uncertain significance
ethA 4328317 c.-844C>T upstream_gene_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407967 p.Leu79Trp missense_variant 0.98 streptomycin Uncertain significance