Run ID: ERR9807015
Sample name:
Date: 18-05-2023 21:26:56
Number of reads: 1479047
Percentage reads mapped: 99.66
Strain: lineage4.4.1.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | inhA p.Ser94Ala (1.00), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Gln497Arg (1.00) |
Pyrazinamide | R | pncA p.Gln10Pro (1.00) |
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Asp94Tyr (1.00) |
Moxifloxacin | R | gyrA p.Asp94Tyr (1.00) |
Ofloxacin | R | gyrA p.Asp94Tyr (1.00) |
Levofloxacin | R | gyrA p.Asp94Tyr (1.00) |
Ciprofloxacin | R | gyrA p.Asp94Tyr (1.00) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | inhA p.Ser94Ala (1.00) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.4 | Euro-American | S;T | None | 1.0 |
lineage4.4.1 | Euro-American (S-type) | S;T | None | 1.0 |
lineage4.4.1.1 | Euro-American | S;Orphans | None | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Tyr | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
inhA | 1674481 | p.Ser94Ala | missense_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289213 | p.Gln10Pro | missense_variant | 1.0 | pyrazinamide |
embB | 4248003 | p.Gln497Arg | missense_variant | 1.0 | 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 | 9138 | p.Gln613Glu | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoC | 762836 | c.-534C>G | upstream_gene_variant | 0.14 |
rpoC | 764936 | p.Gln523Glu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 777416 | c.1065G>T | synonymous_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475954 | n.2297A>C | non_coding_transcript_exon_variant | 1.0 |
rpsA | 1833585 | p.Asp15Gly | missense_variant | 0.97 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.96 |
ndh | 2102990 | p.Val18Ala | missense_variant | 1.0 |
PPE35 | 2168479 | p.Thr712Pro | missense_variant | 1.0 |
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ribD | 2987307 | p.Ala157Pro | missense_variant | 0.17 |
Rv2752c | 3065039 | p.Tyr385Asp | missense_variant | 1.0 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.38 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568779 | c.-100T>C | upstream_gene_variant | 0.97 |
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 1.0 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4249397 | p.Ala962Pro | missense_variant | 0.12 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407790 | p.Ala138Glu | missense_variant | 1.0 |