Run ID: ERR4800084
Sample name:
Date: 20-10-2023 04:19:00
Number of reads: 3902152
Percentage reads mapped: 99.58
Strain: lineage3.1.2
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (0.97) |
| Isoniazid | R | katG p.Ser315Thr (0.99) |
| Ethambutol | R | embA c.-16C>T (0.96) |
| Pyrazinamide | R | pncA c.390_391dupGG (0.96), pncA c.390_391dupGG (0.96) |
| Streptomycin | ||
| Fluoroquinolones | R | gyrA p.Ala90Val (0.97) |
| Moxifloxacin | R | gyrA p.Ala90Val (0.97) |
| Ofloxacin | R | gyrA p.Ala90Val (0.97) |
| Levofloxacin | R | gyrA p.Ala90Val (0.97) |
| Ciprofloxacin | R | gyrA p.Ala90Val (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 |
| lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 1.0 |
| lineage3.1.2 | East-African-Indian | CAS;CAS2 | RD750 | 0.98 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7570 | p.Ala90Val | missense_variant | 0.97 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.97 | rifampicin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid |
| pncA | 2288850 | c.390_391dupGG | frameshift_variant | 0.96 | pyrazinamide, pyrazinamide |
| embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.96 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 0.99 |
| gyrA | 9122 | c.1821C>T | synonymous_variant | 0.97 |
| 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 | 0.99 |
| rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.98 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
| rpoC | 764817 | p.Val483Gly | missense_variant | 0.99 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.98 |
| 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 | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| PPE35 | 2168604 | p.Pro670Leu | missense_variant | 0.95 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2289047 | c.195C>T | synonymous_variant | 0.99 |
| pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
| ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.98 |
| folC | 2746646 | p.Gln318Pro | missense_variant | 0.97 |
| ribD | 2987588 | c.750C>T | synonymous_variant | 0.99 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| embC | 4240190 | p.Pro110Ser | missense_variant | 1.0 |
| embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4245187 | p.Thr652Lys | missense_variant | 0.98 |
| aftB | 4267781 | c.1056C>A | synonymous_variant | 0.98 |
| ubiA | 4269719 | p.Ala39Ser | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 0.99 |
| gid | 4408203 | c.-1A>C | upstream_gene_variant | 0.99 |
