Run ID: SRR25827387
Sample name:
Date: 21-03-2024 06:04:42
Number of reads: 11224147
Percentage reads mapped: 95.65
Strain: lineage3
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00) |
| Isoniazid | R | katG p.Ser315Thr (0.98) |
| Ethambutol | R | embA c.-11C>A (1.00) |
| Pyrazinamide | R | pncA p.Thr135Pro (0.99) |
| Streptomycin | R | rpsL p.Lys88Arg (1.00) |
| Fluoroquinolones | R | gyrA p.Asp94Gly (1.00) |
| Moxifloxacin | R | gyrA p.Asp94Gly (1.00) |
| Ofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Levofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Ciprofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | ethA c.672dupG (0.99), ethA c.672dupG (0.99) |
| 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 | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 0.98 | isoniazid |
| pncA | 2288839 | p.Thr135Pro | missense_variant | 0.99 | pyrazinamide |
| embA | 4243222 | c.-11C>A | upstream_gene_variant | 1.0 | ethambutol |
| ethA | 4326801 | c.672dupG | frameshift_variant | 0.99 | ethionamide, ethionamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 0.99 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| mshA | 575998 | c.652dupG | frameshift_variant | 1.0 |
| mshA | 576002 | c.656delA | frameshift_variant | 1.0 |
| rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.99 |
| rpoB | 760281 | p.Thr159Pro | missense_variant | 0.2 |
| rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.99 |
| 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 |
| mmpS5 | 778892 | p.Leu5Pro | 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 | 2154724 | p.Arg463Leu | missense_variant | 0.99 |
| 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 | 1.0 |
| ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
| Rv2752c | 3065935 | c.256dupC | frameshift_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3449672 | p.Tyr390Ser | missense_variant | 0.95 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fbiB | 3642877 | p.Lys448Arg | missense_variant | 1.0 |
| embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4245227 | c.1995C>T | synonymous_variant | 1.0 |
| embB | 4247015 | p.Ser168Ala | missense_variant | 0.19 |
| embB | 4247702 | p.Pro397Ser | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
