Run ID: ERR1035046
Sample name:
Date: 20-10-2023 23:35:02
Number of reads: 7620364
Percentage reads mapped: 99.46
Strain: lineage4.7;lineage3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.45) |
Isoniazid | R | inhA c.-154G>A (0.45), katG p.Ser315Thr (0.48) |
Ethambutol | R | embB p.Met306Ile (0.57) |
Pyrazinamide | R | pncA p.Gly97Asp (0.43) |
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Ala90Val (0.45) |
Moxifloxacin | R | gyrA p.Ala90Val (0.45) |
Ofloxacin | R | gyrA p.Ala90Val (0.45) |
Levofloxacin | R | gyrA p.Ala90Val (0.45) |
Ciprofloxacin | R | gyrA p.Ala90Val (0.45) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | inhA c.-154G>A (0.45), ethA p.Thr342Lys (0.49) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.55 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.45 |
lineage4.7 | Euro-American (mainly T) | T1;T5 | None | 0.45 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.45 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.45 | rifampicin |
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 0.45 | isoniazid, ethionamide |
katG | 2155167 | p.Ser315Thr | missense_variant | 0.48 | isoniazid |
pncA | 2288952 | p.Gly97Asp | missense_variant | 0.43 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 0.57 | ethambutol |
ethA | 4326449 | p.Thr342Lys | missense_variant | 0.49 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.56 |
gyrA | 8056 | p.Arg252Leu | missense_variant | 0.58 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.56 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.52 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.52 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.56 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.51 |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.38 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.49 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474294 | n.637C>G | non_coding_transcript_exon_variant | 0.45 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.57 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.57 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.57 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.58 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.6 |
thyA | 3074424 | c.48G>T | synonymous_variant | 0.58 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.5 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.58 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.47 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.98 |
embB | 4249732 | c.3219C>G | synonymous_variant | 0.43 |
ethA | 4328212 | c.-740delC | upstream_gene_variant | 0.5 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.58 |
gid | 4407704 | p.Ala167Pro | missense_variant | 0.42 |