Run ID: SRR11828963
Sample name:
Date: 25-01-2024 12:54:51
Number of reads: 4337214
Percentage reads mapped: 99.52
Strain: lineage2.1
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.His445Tyr (1.00) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.Asp1024Asn (1.00) |
| Pyrazinamide | ||
| Streptomycin | ||
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage2 | East-Asian | Beijing | RD105 | 1.0 |
| lineage2.1 | East-Asian (non-Beijing) | None | None | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761139 | p.His445Tyr | missense_variant | 1.0 | rifampicin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| embB | 4249583 | p.Asp1024Asn | missense_variant | 1.0 | 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 | 1.0 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
| rpoC | 765121 | c.1752G>A | synonymous_variant | 0.99 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.99 |
| mmpS5 | 778706 | p.Val67Gly | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| fbiC | 1304443 | p.Ala505Thr | missense_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.99 |
| 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 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| PPE35 | 2169102 | p.Pro504Leu | missense_variant | 0.98 |
| Rv1979c | 2223293 | c.-129A>G | 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 |
| alr | 3841332 | p.Gln30Arg | missense_variant | 1.0 |
| clpC1 | 4040841 | c.-138delG | upstream_gene_variant | 0.99 |
| embC | 4240418 | p.Gly186Cys | missense_variant | 0.99 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4243891 | p.Gly220Glu | missense_variant | 1.0 |
| embB | 4246088 | c.-426A>G | upstream_gene_variant | 0.99 |
| embB | 4248953 | p.Asp814Asn | missense_variant | 1.0 |
| aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
| gid | 4407829 | c.373delC | frameshift_variant | 0.99 |
| gid | 4408276 | c.-74G>A | upstream_gene_variant | 1.0 |
