Run ID: SRR25207318
Sample name:
Date: 28-01-2024 17:08:41
Number of reads: 5549767
Percentage reads mapped: 99.5
Strain: lineage4.5
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Pro483Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Ile (1.00) |
Pyrazinamide | ||
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Asp94Gly (1.00) |
Moxifloxacin | R | gyrA p.Asp94Gly (1.00) |
Ofloxacin | R | gyrA p.Asp94Gly (1.00) |
Levofloxacin | R | gyrA p.Asp94Gly (1.00) |
Ciprofloxacin | R | gyrA p.Asp94Gly (1.00) |
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 |
lineage4.5 | Euro-American | H;T | RD122 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761254 | p.Pro483Leu | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7892 | c.591G>A | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
ccsA | 620029 | c.139C>T | synonymous_variant | 1.0 |
rpoB | 761248 | p.Glu481Ala | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpR5 | 779127 | c.139dupG | frameshift_variant | 0.72 |
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 |
PPE35 | 2170568 | p.Ile15Met | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612398 | p.Ala240Val | missense_variant | 1.0 |
rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 0.98 |
rpoA | 3878613 | c.-106A>C | upstream_gene_variant | 0.12 |
rpoA | 3878614 | c.-107A>C | upstream_gene_variant | 0.23 |
rpoA | 3878619 | c.-112A>C | upstream_gene_variant | 0.25 |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 |
clpC1 | 4038354 | p.Gln784Pro | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.24 |
embB | 4247033 | p.Ser174Arg | missense_variant | 0.19 |
embB | 4247051 | p.Asn180His | missense_variant | 0.14 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407917 | p.Arg96Cys | missense_variant | 1.0 |