Run ID: ERR2516434
Sample name:
Date: 19-10-2023 23:45:01
Number of reads: 3542356
Percentage reads mapped: 99.72
Strain: lineage4.1.4
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.His445Cys (1.00) |
Isoniazid | R | inhA p.Ser94Ala (0.97), katG p.Trp300* (0.98) |
Ethambutol | R | embB p.Met306Val (1.00) |
Pyrazinamide | R | pncA p.Val128Gly (1.00) |
Streptomycin | R | gid c.115delC (1.00) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | R | rrs n.1402C>T (1.00) |
Amikacin | R | rrs n.1402C>T (1.00) |
Capreomycin | R | rrs n.1402C>T (1.00) |
Kanamycin | R | rrs n.1402C>T (1.00) |
Cycloserine | ||
Ethionamide | R | inhA p.Ser94Ala (0.97) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.1 | Euro-American | T;X;H | None | 1.0 |
lineage4.1.4 | Euro-American | T;X;H | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761139 | p.His445Cys | missense_variant | 1.0 | rifampicin |
rrs | 1473247 | n.1402C>T | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
inhA | 1674481 | p.Ser94Ala | missense_variant | 0.97 | isoniazid, ethionamide |
katG | 2155212 | p.Trp300* | stop_gained | 0.98 | isoniazid |
pncA | 2288859 | p.Val128Gly | missense_variant | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
gid | 4408087 | c.115delC | frameshift_variant | 1.0 | streptomycin |
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 |
rpoB | 761559 | p.Thr585Ala | missense_variant | 1.0 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.99 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 778042 | p.Ala147Thr | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471861 | n.16T>C | non_coding_transcript_exon_variant | 1.0 |
rrs | 1473235 | n.1390C>T | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168298 | p.Pro772Leu | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv2752c | 3066058 | p.Cys45Tyr | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.98 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |