Run ID: ERR9806872
Sample name:
Date: 18-05-2023 17:28:24
Number of reads: 1683714
Percentage reads mapped: 99.71
Strain: lineage4.8
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | inhA c.-154G>A (0.95), inhA p.Ser94Ala (1.00), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Pro404Ser (1.00) |
Pyrazinamide | R | pncA c.468_499delGGTGGACCTGACAGCGGGTGTGTCGGCCGATA (1.00) |
Streptomycin | ||
Fluoroquinolones | R | gyrB p.Ile486Leu (1.00) |
Moxifloxacin | R | gyrB p.Ile486Leu (1.00) |
Ofloxacin | R | gyrB p.Ile486Leu (1.00) |
Levofloxacin | R | gyrB p.Ile486Leu (1.00) |
Ciprofloxacin | R | gyrB p.Ile486Leu (1.00) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | inhA c.-154G>A (0.95), 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 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6695 | p.Ile486Leu | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 0.95 | isoniazid, ethionamide |
inhA | 1674481 | p.Ser94Ala | missense_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288742 | c.468_499delGGTGGACCTGACAGCGGGTGTGTCGGCCGATA | frameshift_variant | 1.0 | pyrazinamide |
embB | 4247723 | p.Pro404Ser | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6743 | p.Val502Phe | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpS5 | 779677 | c.-772G>A | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1305471 | c.2541C>T | synonymous_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168867 | c.1746G>A | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
alr | 3840764 | c.657G>C | synonymous_variant | 0.98 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |