TB-Profiler result

Run: ERR6358869
Summary

Run ID: ERR6358869

Sample name:

Date: 2024-04-15T21:43:15.164249

Number of reads: 3205538

Percentage reads mapped: 99.61

Median coverage: 92.0

Strain: lineage4.6.1.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 1.0
lineage4 Euro-American None 1.0
lineage4.6.1.1 Euro-American RD724 1.0
lineage4.6.1 Euro-American (Uganda) RD724 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.Gln525Pro Uncertain significance Mutation from literature
c.643delG Assoc w R High-level resistance
ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol
pyrazinamide pncA c.446dupA Assoc w R
p.His137Pro Assoc w R - Interim
p.Leu4Ser 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 1.0 rifampicin Assoc w R
katG 2154538 p.Gln525Pro missense_variant 0.11 isoniazid Uncertain significance Mutation from literature
katG 2155468 c.643delG frameshift_variant 0.12 isoniazid Assoc w R High-level resistance
pncA 2288795 c.446dupA frameshift_variant 0.14 pyrazinamide Assoc w R
pncA 2288832 p.His137Pro missense_variant 0.14 pyrazinamide Assoc w R - Interim
pncA 2289231 p.Leu4Ser missense_variant 0.16 pyrazinamide Assoc w R
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 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 7539 p.Thr80Ala missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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
hadA 732265 c.336G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
rpoC 767123 p.Val1252Leu 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253754 p.Thr261Pro missense_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
katG 2154681 p.Trp477Tyr missense_variant 1.0 isoniazid
katG 2156100 c.12A>G synonymous_variant 0.28 isoniazid Not assoc w R - Interim
katG 2156110 p.Val1Gly missense_variant 0.14 isoniazid
Rv1979c 2222522 p.Lys215Glu missense_variant 1.0 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2747481 p.Glu40Lys missense_variant 1.0 para-aminosalicylic_acid
Rv2681 2996876 c.138A>C synonymous_variant 1.0 capreomycin Not assoc w R
Rv2752c 3065587 p.Asp202Ala missense_variant 0.99 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3074495 c.-24C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
whiB7 3569029 c.-350A>G upstream_gene_variant 0.99 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Not assoc w R
glpK 4139670 p.Cys29Tyr missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Not assoc w R
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139859 c.-104C>T upstream_gene_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243201 c.-31delC upstream_gene_variant 1.0 ethambutol Uncertain significance
embA 4245184 p.Leu651Arg missense_variant 1.0 ethambutol
ethA 4328329 c.-856C>G upstream_gene_variant 1.0 ethionamide
whiB6 4338378 c.141_143delCGA disruptive_inframe_deletion 1.0 capreomycin
amikacin
kanamycin
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 4408009 p.Val65Gly missense_variant 1.0 streptomycin Uncertain significance