Run ID: ERR1034612
Sample name:
Date: 20-10-2023 22:03:18
Number of reads: 15359853
Percentage reads mapped: 98.45
Strain: lineage3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.99) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embA c.-16C>T (1.00) |
Pyrazinamide | ||
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Ala90Val (0.34) |
Moxifloxacin | R | gyrA p.Ala90Val (0.34) |
Ofloxacin | R | gyrA p.Ala90Val (0.34) |
Levofloxacin | R | gyrA p.Ala90Val (0.34) |
Ciprofloxacin | R | gyrA p.Ala90Val (0.34) |
Aminoglycosides | R | rrs n.1401A>G (0.78) |
Amikacin | R | rrs n.1401A>G (0.78) |
Capreomycin | R | rrs n.1401A>G (0.78) |
Kanamycin | R | rrs n.1401A>G (0.78) |
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.34 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.78 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 1.0 | ethambutol |
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 | 491742 | c.960T>C | synonymous_variant | 1.0 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.99 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.99 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764666 | p.Gly433Ser | missense_variant | 0.99 |
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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2222604 | c.561C>T | synonymous_variant | 0.99 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.99 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.99 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.99 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4246727 | p.Ile72Arg | missense_variant | 0.98 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407959 | p.Ala82Pro | missense_variant | 0.99 |