Run ID: ERR3287855
Sample name:
Date: 20-10-2023 05:51:44
Number of reads: 3483390
Percentage reads mapped: 99.66
Strain: lineage4.3.3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Asp435Tyr (1.00) |
Isoniazid | ||
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Asp94Tyr (0.32) |
Moxifloxacin | R | gyrA p.Asp94Tyr (0.32) |
Ofloxacin | R | gyrA p.Asp94Tyr (0.32) |
Levofloxacin | R | gyrA p.Asp94Tyr (0.32) |
Ciprofloxacin | R | gyrA p.Asp94Tyr (0.32) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | R | tlyA c.311dupG (0.50), tlyA c.311dupG (0.50) |
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | ethA c.672_673dupGC (0.77), ethA c.672_673dupGC (0.77) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Tyr | missense_variant | 0.32 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761109 | p.Asp435Tyr | missense_variant | 1.0 | rifampicin |
tlyA | 1918248 | c.311dupG | frameshift_variant | 0.5 | capreomycin, capreomycin |
ethA | 4326800 | c.672_673dupGC | frameshift_variant | 0.77 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6579 | p.Ser447Tyr | missense_variant | 0.6 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776216 | c.2265G>T | synonymous_variant | 0.99 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2155295 | p.Gly273Cys | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288937 | p.Ala102Val | missense_variant | 1.0 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 |
ahpC | 2726152 | c.-41C>A | upstream_gene_variant | 1.0 |
Rv2752c | 3065824 | p.Pro123Leu | missense_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.99 |
embC | 4240137 | p.Ala92Gly | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243217 | c.-16C>A | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407844 | p.Glu120Ala | missense_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |