Run ID: ERR4813212
Sample name:
Date: 20-10-2023 05:09:13
Number of reads: 3150545
Percentage reads mapped: 99.8
Strain: lineage4.3.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | inhA c.-154G>A (1.00), katG p.Ser315Asn (1.00) |
Ethambutol | ||
Pyrazinamide | R | pncA p.Thr142Lys (0.29) |
Streptomycin | ||
Fluoroquinolones | R | gyrB p.Arg446His (0.29), gyrA p.Gly88Ala (0.12), gyrA p.Asp94Ala (0.46) |
Moxifloxacin | R | gyrB p.Arg446His (0.29), gyrA p.Gly88Ala (0.12), gyrA p.Asp94Ala (0.46) |
Ofloxacin | R | gyrB p.Arg446His (0.29), gyrA p.Gly88Ala (0.12), gyrA p.Asp94Ala (0.46) |
Levofloxacin | R | gyrB p.Arg446His (0.29), gyrA p.Gly88Ala (0.12), gyrA p.Asp94Ala (0.46) |
Ciprofloxacin | R | gyrB p.Arg446His (0.29), gyrA p.Gly88Ala (0.12), gyrA p.Asp94Ala (0.46) |
Aminoglycosides | R | rrs n.1401A>G (0.39) |
Amikacin | R | rrs n.1401A>G (0.39) |
Capreomycin | R | rrs n.1401A>G (0.39) |
Kanamycin | R | rrs n.1401A>G (0.39) |
Cycloserine | ||
Ethionamide | R | inhA c.-154G>A (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 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.2 | Euro-American (LAM) | LAM3 | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6576 | p.Arg446His | missense_variant | 0.29 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7564 | p.Gly88Ala | missense_variant | 0.12 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Ala | missense_variant | 0.46 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.39 | kanamycin, capreomycin, aminoglycosides, amikacin |
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Asn | missense_variant | 1.0 | isoniazid |
pncA | 2288817 | p.Thr142Lys | missense_variant | 0.29 | pyrazinamide |
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 | 490915 | p.Arg45Cys | missense_variant | 1.0 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406441 | c.900G>A | synonymous_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2156334 | c.-223G>C | upstream_gene_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
aftB | 4267879 | p.Val320Met | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |