Run ID: SRR6824457
Sample name:
Date: 20-10-2023 19:39:39
Number of reads: 11381240
Percentage reads mapped: 99.18
Strain: lineage4.5
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB c.1300_1305delATGGAC (0.99) |
| Isoniazid | R | katG p.Ser315Ile (0.35), katG p.Asn138Ser (0.67) |
| Ethambutol | ||
| 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 |
|---|---|---|---|---|
| lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
| lineage4.5 | Euro-American | H;T | RD122 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761104 | c.1300_1305delATGGAC | conservative_inframe_deletion | 0.99 | rifampicin |
| katG | 2155168 | p.Ser315Ile | missense_variant | 0.35 | isoniazid |
| katG | 2155699 | p.Asn138Ser | missense_variant | 0.67 | isoniazid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 5990 | p.Phe251Val | missense_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 7892 | c.591G>A | synonymous_variant | 0.99 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| ccsA | 620029 | c.139C>T | synonymous_variant | 0.99 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| fbiC | 1302973 | p.Pro15Ser | missense_variant | 1.0 |
| Rv1258c | 1406942 | c.396_398delCGC | disruptive_inframe_deletion | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rpsA | 1834914 | p.Lys458Thr | missense_variant | 0.99 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| ndh | 2102941 | c.102G>A | synonymous_variant | 1.0 |
| PPE35 | 2170568 | p.Ile15Met | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| ahpC | 2725933 | c.-260G>A | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 1.0 |
| clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
