Run ID: ERR038755
Sample name:
Date: 20-10-2023 23:46:21
Number of reads: 18083318
Percentage reads mapped: 99.46
Strain: lineage4.1.1.3
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.29), rpoB p.Leu452Pro (0.33) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embA c.-16C>T (0.41), embA c.-11C>A (0.57) |
Pyrazinamide | ||
Streptomycin | R | gid c.115delC (0.24), gid c.102delG (0.44) |
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 |
lineage4.1 | Euro-American | T;X;H | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 1.0 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.29 | rifampicin |
rpoB | 761161 | p.Leu452Pro | missense_variant | 0.33 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.41 | ethambutol |
embA | 4243222 | c.-11C>A | upstream_gene_variant | 0.57 | ethambutol |
gid | 4408087 | c.115delC | frameshift_variant | 0.24 | streptomycin |
gid | 4408100 | c.102delG | frameshift_variant | 0.44 | 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 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475615 | n.1958C>T | non_coding_transcript_exon_variant | 0.98 |
rpsA | 1833684 | p.Arg48Pro | missense_variant | 1.0 |
rpsA | 1834130 | p.Glu197Lys | missense_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyX | 3067901 | c.45C>T | synonymous_variant | 0.99 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
rpoA | 3877964 | p.Arg182Trp | missense_variant | 0.18 |
embC | 4241292 | p.Leu477Arg | missense_variant | 0.62 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.99 |
embA | 4243622 | c.390G>A | synonymous_variant | 1.0 |
embB | 4247106 | p.Pro198His | missense_variant | 0.6 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
ethA | 4326279 | p.Ser399Pro | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407862 | p.Ile114Asn | missense_variant | 0.19 |