Run ID: ERR4796961
Sample name:
Date: 20-10-2023 01:52:57
Number of reads: 8021532
Percentage reads mapped: 99.68
Strain: lineage3
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB c.1279_1284delACCAGC (1.00) |
| Isoniazid | R | katG c.495dupT (1.00) |
| Ethambutol | R | embB p.Met306Val (0.99) |
| Pyrazinamide | R | pncA p.Leu182Ser (0.13), pncA c.63_64delAA (0.40), pncA c.-11A>G (0.13) |
| Streptomycin | ||
| 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 | R | eis c.-14C>T (1.00) |
| Capreomycin | ||
| Kanamycin | R | eis c.-14C>T (1.00) |
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage3 | East-African-Indian | CAS | RD750 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761082 | c.1279_1284delACCAGC | conservative_inframe_deletion | 1.0 | rifampicin |
| katG | 2155616 | c.495dupT | frameshift_variant | 1.0 | isoniazid |
| pncA | 2288697 | p.Leu182Ser | missense_variant | 0.13 | pyrazinamide |
| pncA | 2289177 | c.63_64delAA | frameshift_variant | 0.4 | pyrazinamide |
| pncA | 2289252 | c.-11A>G | upstream_gene_variant | 0.13 | pyrazinamide |
| eis | 2715346 | c.-14C>T | upstream_gene_variant | 1.0 | kanamycin, amikacin |
| embB | 4247429 | p.Met306Val | missense_variant | 0.99 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 6362 | p.Leu375Val | missense_variant | 1.0 |
| gyrB | 6741 | p.Glu501Ala | missense_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 8948 | c.1647G>A | synonymous_variant | 1.0 |
| 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 | 0.99 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| embR | 1416820 | c.528C>T | synonymous_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| PPE35 | 2169192 | p.Ala474Val | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 |
| pncA | 2289139 | c.94_102dupAGCGACTAC | conservative_inframe_insertion | 0.17 |
| pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
| ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| embC | 4242075 | p.Arg738Gln | missense_variant | 0.96 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
