Run ID: ERR2516532
Sample name:
Date: 19-10-2023 23:47:22
Number of reads: 2634944
Percentage reads mapped: 99.54
Strain: lineage4.1.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.His445Ser (0.95) |
Isoniazid | R | katG c.1571dupT (1.00), ahpC c.-48G>A (1.00), ahpC c.-39C>T (1.00) |
Ethambutol | R | embB p.Asp354Ala (1.00), embB p.Gln497Pro (1.00) |
Pyrazinamide | R | pncA c.-11A>G (1.00) |
Streptomycin | R | rpsL p.Lys88Gln (1.00) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | R | thyA p.Phe152Val (0.90) |
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.1 | Euro-American | T;X;H | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Ser | missense_variant | 0.95 | rifampicin |
rpsL | 781821 | p.Lys88Gln | missense_variant | 1.0 | streptomycin |
katG | 2154540 | c.1571dupT | frameshift_variant | 1.0 | isoniazid |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 1.0 | pyrazinamide |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 1.0 | isoniazid |
ahpC | 2726154 | c.-39C>T | upstream_gene_variant | 1.0 | isoniazid |
thyA | 3074018 | p.Phe152Val | missense_variant | 0.9 | para-aminosalicylic_acid |
embB | 4247574 | p.Asp354Ala | missense_variant | 1.0 | ethambutol |
embB | 4248003 | p.Gln497Pro | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6052 | p.Ile271Met | missense_variant | 1.0 |
gyrB | 7221 | p.Ser661Thr | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 766653 | p.Ser1095Phe | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1416699 | p.Leu217Val | missense_variant | 1.0 |
embR | 1417416 | c.-69G>A | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
inhA | 1673865 | c.-337C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
ethA | 4327059 | p.Gly139Ser | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408275 | c.-73G>C | upstream_gene_variant | 1.0 |