Run ID: ERR3335786
Sample name:
Date: 21-10-2023 15:22:04
Number of reads: 8180582
Percentage reads mapped: 99.47
Strain: lineage3
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Phe (0.99) |
| Isoniazid | R | katG c.678_679dupGC (0.97) |
| Ethambutol | R | embA c.-16C>T (0.99), embB p.Met306Ile (0.99) |
| Pyrazinamide | R | pncA c.194_203delCCTCGTCGTG (0.98) |
| Streptomycin | R | rrs n.517C>T (0.97) |
| Fluoroquinolones | R | gyrA p.Gly88Cys (0.97) |
| Moxifloxacin | R | gyrA p.Gly88Cys (0.97) |
| Ofloxacin | R | gyrA p.Gly88Cys (0.97) |
| Levofloxacin | R | gyrA p.Gly88Cys (0.97) |
| Ciprofloxacin | R | gyrA p.Gly88Cys (0.97) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage3 | East-African-Indian | CAS | RD750 | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7563 | p.Gly88Cys | missense_variant | 0.97 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Phe | missense_variant | 0.99 | rifampicin |
| rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.97 | streptomycin |
| katG | 2155432 | c.678_679dupGC | frameshift_variant | 0.97 | isoniazid |
| pncA | 2289038 | c.194_203delCCTCGTCGTG | frameshift_variant | 0.98 | pyrazinamide |
| embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.99 | ethambutol |
| embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | 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 | 8948 | c.1647G>A | synonymous_variant | 0.98 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
| rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_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 |
| katG | 2154671 | p.Ser481Ala | missense_variant | 0.97 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.99 |
| ahpC | 2725937 | c.-256T>G | upstream_gene_variant | 0.96 |
| ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
| ahpC | 2726116 | c.-77T>A | upstream_gene_variant | 0.99 |
| thyA | 3074373 | p.Gln33His | missense_variant | 0.97 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fprA | 3474123 | c.117G>A | synonymous_variant | 0.99 |
| embC | 4242075 | p.Arg738Gln | missense_variant | 0.99 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embB | 4248992 | p.Asn827Asp | missense_variant | 0.99 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
