Run ID: ERR4810833
Sample name:
Date: 20-10-2023 00:17:55
Number of reads: 6360221
Percentage reads mapped: 99.21
Strain: lineage4.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Asp435Tyr (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | ||
Pyrazinamide | R | pncA p.Tyr34* (0.15) |
Streptomycin | R | gid c.137dupA (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 |
lineage4.2 | Euro-American | H;T;LAM | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761109 | p.Asp435Tyr | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289140 | p.Tyr34* | stop_gained | 0.15 | pyrazinamide |
gid | 4408065 | c.137dupA | 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 | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
embR | 1417507 | c.-160A>G | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
inhA | 1674786 | c.585G>A | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101747 | c.1296C>T | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 |
fbiD | 3339343 | p.Gly76Ser | missense_variant | 1.0 |
fbiD | 3339349 | p.Asp78Asn | missense_variant | 1.0 |
Rv3083 | 3449771 | p.Pro423Leu | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
alr | 3841499 | c.-79C>T | upstream_gene_variant | 1.0 |
clpC1 | 4040872 | c.-168C>T | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
ethA | 4328322 | c.-849G>A | upstream_gene_variant | 1.0 |
whiB6 | 4338309 | c.213T>C | synonymous_variant | 1.0 |
whiB6 | 4338505 | p.Ala6Glu | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |