Run ID: SRR25515487
Sample name:
Date: 08-03-2024 05:01:54
Number of reads: 3808335
Percentage reads mapped: 99.62
Strain: lineage2.2.2
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Leu430Pro (0.99) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.Met306Ile (1.00) |
| Pyrazinamide | R | pncA p.Gly108Arg (1.00) |
| Streptomycin | R | rpsL p.Lys43Arg (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 | R | rrs n.1401A>G (1.00) |
| Amikacin | R | rrs n.1401A>G (1.00) |
| Capreomycin | R | rrs n.1401A>G (1.00) |
| Kanamycin | R | rrs n.1401A>G (1.00) |
| Cycloserine | ||
| Ethionamide | ||
| 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 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761095 | p.Leu430Pro | missense_variant | 0.99 | rifampicin |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2288920 | p.Gly108Arg | missense_variant | 1.0 | pyrazinamide |
| embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 5082 | c.-158_-157insC | upstream_gene_variant | 1.0 |
| gyrB | 6773 | p.Gly512Arg | missense_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 0.99 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| rpoB | 760309 | p.Val168Gly | missense_variant | 1.0 |
| rpoB | 762370 | p.Leu855Ser | missense_variant | 1.0 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.99 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.98 |
| mmpR5 | 779138 | p.Arg50Gln | missense_variant | 0.99 |
| 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 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| 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 |
| Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.97 |
| embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
| aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
| ethA | 4326035 | p.Phe480Ser | missense_variant | 0.98 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
| gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |
