Run ID: ERR11488931
Sample name:
Date: 08-01-2024 17:44:52
Number of reads: 3012647
Percentage reads mapped: 99.8
Strain: lineage4.3.4.2.1
Drug-resistance: XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00), ahpC c.-52C>T (1.00) |
Ethambutol | R | embA c.-16C>T (1.00), embB p.Met306Leu (1.00) |
Pyrazinamide | R | pncA c.419delG (1.00) |
Streptomycin | R | rpsL p.Lys43Arg (1.00) |
Fluoroquinolones | R | gyrA p.Ala90Val (1.00) |
Moxifloxacin | R | gyrA p.Ala90Val (1.00) |
Ofloxacin | R | gyrA p.Ala90Val (1.00) |
Levofloxacin | R | gyrA p.Ala90Val (1.00) |
Ciprofloxacin | R | gyrA p.Ala90Val (1.00) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | ethA c.32delG (1.00), ethA c.32delG (1.00) |
Clofazimine | R | mmpR5 p.Ser68Gly (0.21) |
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | R | mmpR5 p.Ser68Gly (0.21) |
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 1.0 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 1.0 |
lineage4.3.4.2.1 | Euro-American (LAM) | LAM11 | RD174 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
mmpR5 | 779191 | p.Ser68Gly | missense_variant | 0.21 | clofazimine, bedaquiline |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288822 | c.419delG | frameshift_variant | 1.0 | pyrazinamide |
ahpC | 2726141 | c.-52C>T | upstream_gene_variant | 1.0 | isoniazid |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 1.0 | ethambutol |
embB | 4247429 | p.Met306Leu | missense_variant | 1.0 | ethambutol |
ethA | 4327441 | c.32delG | frameshift_variant | 1.0 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6140 | p.Val301Leu | missense_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8795 | c.1494C>T | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoC | 764703 | p.Lys445Arg | missense_variant | 1.0 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpR5 | 779215 | p.Gln76* | stop_gained | 0.34 |
mmpR5 | 779284 | p.Ala99Thr | missense_variant | 0.34 |
mmpR5 | 779363 | p.Leu125Pro | missense_variant | 0.23 |
mmpS5 | 779609 | c.-704C>T | upstream_gene_variant | 1.0 |
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289909 | c.-668G>A | upstream_gene_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 |
alr | 3840719 | c.702A>G | synonymous_variant | 1.0 |
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 |