Run ID: ERR4830821
Sample name:
Date: 20-10-2023 06:47:10
Number of reads: 4128253
Percentage reads mapped: 99.53
Strain: lineage4.2.2.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.His445Cys (0.86), rpoB p.Ser450Leu (0.17) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Ile (0.84), embB p.Met306Ile (0.15) |
Pyrazinamide | R | pncA c.-11A>G (0.19) |
Streptomycin | R | gid p.Gly69Asp (0.17) |
Fluoroquinolones | R | gyrA p.Ala90Val (0.83) |
Moxifloxacin | R | gyrA p.Ala90Val (0.83) |
Ofloxacin | R | gyrA p.Ala90Val (0.83) |
Levofloxacin | R | gyrA p.Ala90Val (0.83) |
Ciprofloxacin | R | gyrA p.Ala90Val (0.83) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
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 | 1.0 |
lineage4.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.99 |
lineage4.2.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.83 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761139 | p.His445Cys | missense_variant | 0.86 | rifampicin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.17 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 0.19 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 0.84 | ethambutol |
embB | 4247431 | p.Met306Ile | missense_variant | 0.15 | ethambutol |
gid | 4407997 | p.Gly69Asp | missense_variant | 0.17 | streptomycin |
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 | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 576077 | c.730C>T | synonymous_variant | 1.0 |
rpoB | 761489 | c.1683G>A | synonymous_variant | 1.0 |
rpoC | 764397 | p.Leu343Arg | missense_variant | 0.74 |
rpoC | 766488 | p.Pro1040Arg | missense_variant | 0.12 |
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 |
tlyA | 1918334 | p.Glu132Val | missense_variant | 0.88 |
katG | 2154710 | p.Thr468Pro | missense_variant | 0.2 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518546 | p.Met144Ile | missense_variant | 0.82 |
ahpC | 2726146 | c.-47_-46insT | upstream_gene_variant | 0.16 |
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 1.0 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449623 | c.1120_1121insT | frameshift_variant | 0.85 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4249680 | p.Asp1056Ala | missense_variant | 0.89 |
ethA | 4326038 | p.Arg479Pro | missense_variant | 0.81 |
ethA | 4327472 | c.2T>G | start_lost | 0.2 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407733 | p.Gly157Val | missense_variant | 0.85 |