Run ID: SRR2469373
Sample name:
Date: 21-10-2023 01:22:31
Number of reads: 4348036
Percentage reads mapped: 99.48
Strain: lineage4.1.1.3.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ile491Phe (0.99) |
Isoniazid | ||
Ethambutol | R | embB p.Met306Ile (0.99) |
Pyrazinamide | R | pncA p.Ala146Val (0.17), pncA p.Val125Gly (0.13), pncA p.Val7Leu (0.17) |
Streptomycin | R | gid c.102delG (1.00) |
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 | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.1 | Euro-American | T;X;H | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 1.0 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 1.0 |
lineage4.1.1.3.1 | Euro-American (X-type) | X1;X3 | RD193 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761277 | p.Ile491Phe | missense_variant | 0.99 | rifampicin |
pncA | 2288805 | p.Ala146Val | missense_variant | 0.17 | pyrazinamide |
pncA | 2288868 | p.Val125Gly | missense_variant | 0.13 | pyrazinamide |
pncA | 2289223 | p.Val7Leu | missense_variant | 0.17 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | ethambutol |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | 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 | 9304 | p.Gly668Asp | missense_variant | 0.99 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.99 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303601 | p.Glu224Gly | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154695 | p.Val473Leu | missense_variant | 0.98 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289121 | p.Tyr41Asp | missense_variant | 0.18 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 |
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 |
aftB | 4269540 | c.-704C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |