Run ID: ERR1034611
Sample name:
Date: 20-10-2023 22:03:14
Number of reads: 25602700
Percentage reads mapped: 99.66
Strain: lineage4.8
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | fabG1 c.-15C>T (0.96), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Ile (1.00), embB p.Gly406Asp (0.95) |
Pyrazinamide | R | pncA p.Gly97Ser (0.96) |
Streptomycin | R | rpsL p.Lys43Arg (0.96) |
Fluoroquinolones | R | gyrB p.Ser447Phe (0.97) |
Moxifloxacin | R | gyrB p.Ser447Phe (0.97) |
Ofloxacin | R | gyrB p.Ser447Phe (0.97) |
Levofloxacin | R | gyrB p.Ser447Phe (0.97) |
Ciprofloxacin | R | gyrB p.Ser447Phe (0.97) |
Aminoglycosides | R | rrs n.1401A>G (0.97) |
Amikacin | R | rrs n.1401A>G (0.97) |
Capreomycin | R | rrs n.1401A>G (0.97) |
Kanamycin | R | rrs n.1401A>G (0.97) |
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (0.96), ethA c.299delT (0.94), ethA c.299delT (0.94) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 0.96 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6579 | p.Ser447Phe | missense_variant | 0.97 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.96 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.97 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.96 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288953 | p.Gly97Ser | missense_variant | 0.96 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
embB | 4247730 | p.Gly406Asp | missense_variant | 0.95 | ethambutol |
ethA | 4327174 | c.299delT | frameshift_variant | 0.94 | ethionamide, ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
rpoC | 764616 | p.Asn416Ser | missense_variant | 0.96 |
rpoC | 765331 | c.1962C>T | synonymous_variant | 0.96 |
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 | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.95 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.95 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3087759 | c.942delC | frameshift_variant | 0.87 |
ald | 3087805 | p.Trp329* | stop_gained | 0.11 |
Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 0.24 |
Rv3083 | 3448500 | c.-4A>G | upstream_gene_variant | 0.19 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.96 |