Run ID: ERR2513553
Sample name:
Date: 20-10-2023 10:57:24
Number of reads: 1935790
Percentage reads mapped: 99.6
Strain: lineage4;lineage3
Drug-resistance: Other
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | ||
Ethambutol | R | embB p.Ala313Val (0.15) |
Pyrazinamide | ||
Streptomycin | R | gid p.Gly71* (0.80) |
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 | 0.9 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.08 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
embB | 4247451 | p.Ala313Val | missense_variant | 0.15 | ethambutol |
gid | 4407992 | p.Gly71* | stop_gained | 0.8 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5222 | c.-18G>T | upstream_gene_variant | 0.93 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7601 | c.300C>G | synonymous_variant | 0.92 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.79 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.87 |
rpoB | 762051 | p.His749Tyr | missense_variant | 0.89 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.93 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.98 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.89 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1473609 | n.-49G>C | upstream_gene_variant | 0.93 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.95 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.95 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.89 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.88 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.93 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.93 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.94 |
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 | 0.9 |