Run ID: ERR4800090
Sample name:
Date: 20-10-2023 04:19:52
Number of reads: 4095746
Percentage reads mapped: 99.52
Strain: lineage4.2.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (0.99) |
Ethambutol | R | embB p.Gly406Ser (0.99) |
Pyrazinamide | R | pncA c.417dupG (0.98), pncA c.417dupG (0.98) |
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Asp94Gly (0.98) |
Moxifloxacin | R | gyrA p.Asp94Gly (0.98) |
Ofloxacin | R | gyrA p.Asp94Gly (0.98) |
Levofloxacin | R | gyrA p.Asp94Gly (0.98) |
Ciprofloxacin | R | gyrA p.Asp94Gly (0.98) |
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 | 0.99 |
lineage4.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid |
pncA | 2288824 | c.417dupG | frameshift_variant | 0.98 | pyrazinamide, pyrazinamide |
embB | 4247729 | p.Gly406Ser | missense_variant | 0.99 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5078 | c.-162_-161insG | upstream_gene_variant | 0.99 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 576077 | c.730C>T | synonymous_variant | 0.99 |
rpoB | 759939 | p.Pro45Ser | missense_variant | 1.0 |
rpoB | 761855 | c.2049C>T | synonymous_variant | 0.98 |
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 |
rrl | 1475518 | n.1861A>G | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 0.96 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.98 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
embC | 4242223 | c.2361C>G | synonymous_variant | 0.97 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243217 | c.-16C>A | upstream_gene_variant | 1.0 |
embA | 4246429 | p.Ala1066Val | missense_variant | 0.98 |
ethA | 4327343 | p.Thr44Ile | missense_variant | 1.0 |
ethA | 4327845 | c.-372G>T | upstream_gene_variant | 1.0 |
ethA | 4328438 | c.-965C>A | upstream_gene_variant | 0.99 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407740 | c.462dupG | frameshift_variant | 0.98 |