TB-Profiler result

Run: ERR4812883
Summary

Run ID: ERR4812883

Sample name:

Date: 2024-10-05T12:39:56.589604

Number of reads: 3172809

Percentage reads mapped: 99.81

Median coverage: 96.0

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 0.17
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 embB p.Asp354Ala Assoc w R
pyrazinamide pncA p.Thr135Pro 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 0.84 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.8 isoniazid Assoc w R High-level resistance
pncA 2288839 p.Thr135Pro missense_variant 0.81 pyrazinamide Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.82 ethambutol 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
gyrA 7362 p.Glu21Gln missense_variant 0.86 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.88 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.84 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575837 c.490C>T synonymous_variant 0.91 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
rpoB 761889 p.Val695Leu missense_variant 0.83 rifampicin Uncertain significance
rpoC 764666 p.Gly433Ser missense_variant 0.87 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 0.81 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777875 c.605delG frameshift_variant 0.91 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpR5 779181 c.198dupG frameshift_variant 0.89 bedaquiline Assoc w R
clofazimine Assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.9 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.82 linezolid Not assoc w R - Interim
Rv1129c 1253568 p.Thr323Ala missense_variant 0.83 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.85 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.92 capreomycin Not assoc w R
ndh 2101831 c.1212G>A synonymous_variant 0.88 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
katG 2156173 c.-62C>A upstream_gene_variant 0.91 isoniazid Uncertain significance
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.81 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.81 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726141 c.-52C>A upstream_gene_variant 0.85 isoniazid Uncertain significance
Rv2752c 3065517 c.675C>T synonymous_variant 0.84 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
thyA 3074495 c.-24C>T upstream_gene_variant 0.9 para-aminosalicylic_acid
Rv3236c 3612219 p.Val300Ile missense_variant 0.86 pyrazinamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.81 ethambutol Not assoc w R
ethA 4326458 p.Ile339Ser missense_variant 0.9 ethionamide Uncertain significance
ethA 4328317 c.-844C>T upstream_gene_variant 0.86 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 0.87 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.88 kanamycin
capreomycin
amikacin
gid 4407967 p.Leu79Trp missense_variant 0.82 streptomycin Uncertain significance