Run ID: ERR4813789
Sample name:
Date: 20-10-2023 14:54:26
Number of reads: 3216322
Percentage reads mapped: 99.6
Strain: lineage4.1.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.74) |
Isoniazid | R | fabG1 c.-15C>T (0.72), ahpC c.-57C>T (0.77) |
Ethambutol | R | embB p.Met306Ile (0.81) |
Pyrazinamide | R | pncA c.314dupG (0.73), pncA c.314dupG (0.73) |
Streptomycin | ||
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (0.72) |
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 | 0.95 |
lineage4.1.2 | Euro-American | T;H | None | 0.95 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.94 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.74 | rifampicin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.72 | isoniazid, ethionamide |
pncA | 2288927 | c.314dupG | frameshift_variant | 0.73 | pyrazinamide, pyrazinamide |
ahpC | 2726136 | c.-57C>T | upstream_gene_variant | 0.77 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 0.81 | ethambutol |
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 | 1.0 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.9 |
mshA | 575679 | p.Asn111Ser | missense_variant | 0.95 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.92 |
rpoB | 761550 | p.Ser582Ala | missense_variant | 0.88 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.97 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.99 |
Rv1258c | 1407489 | c.-149G>A | upstream_gene_variant | 0.82 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2155514 | p.Lys200Glu | missense_variant | 0.78 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.92 |
Rv2752c | 3066299 | c.-108C>T | upstream_gene_variant | 0.78 |
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 | 0.92 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |