Run ID: ERR2510340
Sample name:
Date: 20-10-2023 07:10:55
Number of reads: 1798884
Percentage reads mapped: 99.68
Strain: lineage4.9;lineage3
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.24) |
Isoniazid | R | katG p.Ser315Thr (0.17) |
Ethambutol | R | embB p.Met306Val (0.14) |
Pyrazinamide | R | pncA p.Pro54Leu (0.17) |
Streptomycin | R | rpsL p.Lys43Arg (0.17) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
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 | 0.83 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.17 |
lineage4.9 | Euro-American (H37Rv-like) | T1 | None | 0.15 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.24 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.17 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.17 | isoniazid |
pncA | 2289081 | p.Pro54Leu | missense_variant | 0.17 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.14 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 6463 | c.-839C>T | upstream_gene_variant | 0.9 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.92 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.83 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.82 |
mshA | 576400 | c.1053C>T | synonymous_variant | 0.18 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.88 |
rpoB | 761461 | p.Arg552Leu | missense_variant | 0.18 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.91 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.89 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.84 |
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 | 0.95 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.83 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.81 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.79 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.94 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.93 |
fbiB | 3642877 | p.Lys448Arg | missense_variant | 0.74 |
rpoA | 3877536 | c.972C>T | synonymous_variant | 0.13 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.9 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.87 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.73 |