Run ID: ERR4797587
Sample name:
Date: 20-10-2023 02:27:38
Number of reads: 4087028
Percentage reads mapped: 99.55
Strain: lineage4.2.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.His445Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embA c.-12C>T (1.00), embB p.Met306Leu (0.99) |
Pyrazinamide | R | pncA p.Arg121Pro (1.00) |
Streptomycin | R | gid p.Gln125* (0.99) |
Fluoroquinolones | R | gyrA p.Ala90Val (1.00) |
Moxifloxacin | R | gyrA p.Ala90Val (1.00) |
Ofloxacin | R | gyrA p.Ala90Val (1.00) |
Levofloxacin | R | gyrA p.Ala90Val (1.00) |
Ciprofloxacin | R | gyrA p.Ala90Val (1.00) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | ethA c.1016_1018delTTA (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 |
lineage4.2 | Euro-American | H;T;LAM | None | 1.0 |
lineage4.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.87 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761140 | p.His445Leu | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288880 | p.Arg121Pro | missense_variant | 1.0 | pyrazinamide |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol |
embB | 4247429 | p.Met306Leu | missense_variant | 0.99 | ethambutol |
ethA | 4326455 | c.1016_1018delTTA | disruptive_inframe_deletion | 1.0 | ethionamide |
gid | 4407830 | p.Gln125* | stop_gained | 0.99 | 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 |
mshA | 576077 | c.730C>T | synonymous_variant | 1.0 |
rpoC | 762722 | c.-648C>T | upstream_gene_variant | 1.0 |
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 |
inhA | 1674135 | c.-67C>T | upstream_gene_variant | 0.92 |
rpsA | 1834689 | p.Ser383Ile | missense_variant | 0.21 |
rpsA | 1834985 | c.1445dupG | frameshift_variant&stop_lost&splice_region_variant | 0.22 |
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 | 1.0 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 1.0 |
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 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |