Run ID: SRR671824
Sample name:
Date: 20-10-2023 21:49:17
Number of reads: 5598838
Percentage reads mapped: 99.58
Strain: lineage2.2.2
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00), rpoB p.Pro454Leu (0.99) |
| Isoniazid | R | fabG1 c.-15C>T (0.99) |
| Ethambutol | R | embB p.Met306Leu (0.99) |
| Pyrazinamide | R | pncA c.422delA (0.98), pncA c.422delA (0.98) |
| Streptomycin | R | rpsL p.Lys43Arg (1.00) |
| Fluoroquinolones | R | gyrA p.Asp94Gly (0.97) |
| Moxifloxacin | R | gyrA p.Asp94Gly (0.97) |
| Ofloxacin | R | gyrA p.Asp94Gly (0.97) |
| Levofloxacin | R | gyrA p.Asp94Gly (0.97) |
| Ciprofloxacin | R | gyrA p.Asp94Gly (0.97) |
| Aminoglycosides | R | rrs n.1402C>T (1.00) |
| Amikacin | R | rrs n.1402C>T (1.00) |
| Capreomycin | R | rrs n.1402C>T (1.00) |
| Kanamycin | R | rrs n.1402C>T (1.00) |
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-15C>T (0.99) |
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage2 | East-Asian | Beijing | RD105 | 1.0 |
| lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
| lineage2.2.2 | East-Asian (Beijing) | Beijing-RD105/RD207 | RD105;RD207 | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Gly | missense_variant | 0.97 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| rpoB | 761167 | p.Pro454Leu | missense_variant | 0.99 | rifampicin |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
| rrs | 1473247 | n.1402C>T | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.99 | isoniazid, ethionamide |
| pncA | 2288819 | c.422delA | frameshift_variant | 0.98 | pyrazinamide, pyrazinamide |
| embB | 4247429 | p.Met306Leu | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 0.99 |
| rpoB | 761583 | p.His593Tyr | missense_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 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| katG | 2155607 | p.Gly169Ser | missense_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| Rv1979c | 2223256 | c.-92C>A | upstream_gene_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| folC | 2747470 | p.Ile43Ala | missense_variant | 0.99 |
| Rv2752c | 3065072 | p.Gly374Arg | missense_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4243195 | c.-37delT | upstream_gene_variant | 1.0 |
| embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
| aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
| ethA | 4326356 | p.Met373Thr | missense_variant | 0.98 |
| whiB6 | 4338365 | p.Cys53Gly | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 0.98 |
| gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |
