Run ID: ERR4799311
Sample name:
Date: 20-10-2023 03:46:43
Number of reads: 4309426
Percentage reads mapped: 99.47
Strain: lineage4.2.2.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.93) |
Isoniazid | R | katG p.Ser315Thr (0.99), ahpC c.-48G>A (0.97) |
Ethambutol | R | embB p.Met306Ile (0.97) |
Pyrazinamide | R | pncA c.303_314delAGCGTACAGCGG (0.96) |
Streptomycin | R | rpsL p.Lys43Arg (0.98) |
Fluoroquinolones | R | gyrA p.Asp94Gly (1.00) |
Moxifloxacin | R | gyrA p.Asp94Gly (1.00) |
Ofloxacin | R | gyrA p.Asp94Gly (1.00) |
Levofloxacin | R | gyrA p.Asp94Gly (1.00) |
Ciprofloxacin | R | gyrA p.Asp94Gly (1.00) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | ethA p.Cys253* (0.98) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.2 | Euro-American | H;T;LAM | None | 0.98 |
lineage4.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.98 |
lineage4.2.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.98 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.93 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.98 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid |
pncA | 2288927 | c.303_314delAGCGTACAGCGG | disruptive_inframe_deletion | 0.96 | pyrazinamide |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 0.97 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 0.97 | ethambutol |
ethA | 4326715 | p.Cys253* | stop_gained | 0.98 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8688 | p.Ala463Ser | missense_variant | 0.95 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 576077 | c.730C>T | synonymous_variant | 0.99 |
rpoB | 761489 | c.1683G>A | synonymous_variant | 0.99 |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 0.99 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.98 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.99 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |