Run ID: SRR25515758
Sample name:
Date: 14-02-2024 13:00:25
Number of reads: 7444950
Percentage reads mapped: 99.58
Strain: lineage4.4.2
Drug-resistance: HR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | ||
| Isoniazid | R | katG p.Gly285Asp (0.99) |
| Ethambutol | ||
| Pyrazinamide | ||
| Streptomycin | R | rpsL p.Lys43Arg (1.00) |
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
| lineage4.4 | Euro-American | S;T | None | 0.99 |
| lineage4.4.2 | Euro-American | T1;T2 | None | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
| katG | 2155258 | p.Gly285Asp | missense_variant | 0.99 | isoniazid |
| 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 | 0.99 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| fbiC | 1304880 | c.1950C>T | synonymous_variant | 0.99 |
| Rv1258c | 1406692 | p.Arg217Cys | missense_variant | 0.99 |
| Rv1258c | 1407053 | p.Tyr96* | stop_gained | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrl | 1475974 | n.2317A>G | non_coding_transcript_exon_variant | 0.99 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| Rv2752c | 3066099 | p.Met31Ile | missense_variant | 0.97 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3448348 | c.-156G>A | upstream_gene_variant | 0.98 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fbiA | 3641307 | p.Met255Ile | missense_variant | 0.99 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embB | 4246508 | c.-6G>A | upstream_gene_variant | 0.99 |
| embB | 4247249 | p.Gly246Arg | missense_variant | 0.99 |
| aftB | 4268928 | c.-92C>T | upstream_gene_variant | 0.98 |
| aftB | 4269375 | c.-539G>A | upstream_gene_variant | 0.99 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
