Run ID: ERR9806731
Sample name:
Date: 18-05-2023 14:23:39
Number of reads: 109673
Percentage reads mapped: 99.19
Strain: lineage4.9;lineage4.3.2.1
Drug-resistance: RR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | ||
Ethambutol | ||
Pyrazinamide | R | pncA p.His82Tyr (0.33) |
Streptomycin | ||
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | T1 | None | 0.93 |
lineage4.3.2 | Euro-American (LAM) | LAM3 | None | 0.09 |
lineage4.3.2.1 | Euro-American (LAM) | LAM3 | RD761 | 0.12 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
pncA | 2288998 | p.His82Tyr | missense_variant | 0.33 | pyrazinamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 7022 | p.Leu595Val | missense_variant | 0.5 |
gyrA | 7222 | c.-80C>T | upstream_gene_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 | 491460 | p.Asp226Glu | missense_variant | 0.33 |
ccsA | 620205 | c.315G>A | synonymous_variant | 1.0 |
ccsA | 620216 | p.Asn109Ser | missense_variant | 0.67 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.67 |
rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289083 | c.159C>T | synonymous_variant | 0.5 |
Rv2752c | 3064826 | p.Asp456Tyr | missense_variant | 0.5 |
Rv3083 | 3448586 | p.Pro28Leu | missense_variant | 0.5 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |