TB-Profiler result

Run: ERR2706913
Summary

Run ID: ERR2706913

Sample name:

Date: 2024-04-16T02:15:25.502884

Number of reads: 1481709

Percentage reads mapped: 99.7

Median coverage: 38.0

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) 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.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Pro404Ser Uncertain significance Mutation from literature
pyrazinamide pncA p.Ser67Pro Assoc w R
p.Thr61Pro Assoc w R - Interim
streptomycin rrs n.514A>C Assoc w R
gid c.386delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
thyA p.Pro224Leu Mutation from literature
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 761110 p.Asp435Val missense_variant 0.98 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289043 p.Ser67Pro missense_variant 0.38 pyrazinamide Assoc w R
pncA 2289061 p.Thr61Pro missense_variant 0.57 pyrazinamide Assoc w R - Interim
thyX 3067961 c.-16C>T upstream_gene_variant 0.98 para-aminosalicylic_acid Mutation from literature
thyA 3073801 p.Pro224Leu missense_variant 1.0 para-aminosalicylic_acid Mutation from literature
embB 4247723 p.Pro404Ser missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
gid 4407816 c.386delG frameshift_variant 1.0 streptomycin Assoc w R
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
gyrB 5452 p.Glu71Asp missense_variant 0.37 levofloxacin Uncertain significance
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
hadA 732110 p.Cys61Gly missense_variant 0.97 isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472081 n.236C>T non_coding_transcript_exon_variant 0.43 streptomycin
kanamycin
capreomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ubiA 4269124 p.Ala237Val missense_variant 0.59 ethambutol Uncertain significance
ubiA 4269719 p.Ala39Ser missense_variant 0.21 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R