Run ID: SRR5341448
Sample name:
Date: 20-10-2023 18:49:59
Number of reads: 5355750
Percentage reads mapped: 94.82
Strain: lineage3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Gln432Glu (1.00) |
Isoniazid | R | katG c.-5536_*5986del (1.00) |
Ethambutol | R | embB p.Met306Ile (1.00) |
Pyrazinamide | R | pncA c.-11A>G (1.00) |
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Asp94Gly (1.00) |
Moxifloxacin | R | gyrA p.Asp94Gly (1.00) |
Ofloxacin | R | gyrA p.Asp94Gly (1.00) |
Levofloxacin | R | gyrA p.Asp94Gly (1.00) |
Ciprofloxacin | R | gyrA p.Asp94Gly (1.00) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761100 | p.Gln432Glu | missense_variant | 1.0 | rifampicin |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
katG | 2147902 | c.-5536_*5986del | transcript_ablation | 1.0 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6265 | p.Asp342Glu | missense_variant | 1.0 |
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 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
rpoB | 760929 | p.Val375Leu | missense_variant | 0.61 |
rpoB | 762130 | c.2326_2331dupGCCGAC | conservative_inframe_insertion | 0.18 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.99 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1407521 | c.-181C>T | upstream_gene_variant | 0.99 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834347 | p.Arg269Leu | missense_variant | 0.17 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.99 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
ahpC | 2726116 | c.-77T>G | 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 |
clpC1 | 4038883 | p.Gly608Ser | missense_variant | 1.0 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407734 | p.Gly157Trp | missense_variant | 0.11 |
gid | 4408281 | c.-79C>T | upstream_gene_variant | 1.0 |