Run ID: SRR5341320
Sample name:
Date: 20-10-2023 18:53:00
Number of reads: 12094819
Percentage reads mapped: 96.23
Strain: lineage3
Drug-resistance: Other
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | ||
| Isoniazid | ||
| Ethambutol | ||
| Pyrazinamide | R | pncA p.Ser164Pro (0.23), pncA p.Val155Gly (0.65) |
| Streptomycin | R | gid c.102delG (1.00) |
| Fluoroquinolones | R | gyrB p.Glu501Asp (0.70), gyrA p.Asp89Asn (0.21), gyrA p.Ser91Pro (0.11) |
| Moxifloxacin | R | gyrB p.Glu501Asp (0.70), gyrA p.Asp89Asn (0.21), gyrA p.Ser91Pro (0.11) |
| Ofloxacin | R | gyrB p.Glu501Asp (0.70), gyrA p.Asp89Asn (0.21), gyrA p.Ser91Pro (0.11) |
| Levofloxacin | R | gyrB p.Glu501Asp (0.70), gyrA p.Asp89Asn (0.21), gyrA p.Ser91Pro (0.11) |
| Ciprofloxacin | R | gyrB p.Glu501Asp (0.70), gyrA p.Asp89Asn (0.21), gyrA p.Ser91Pro (0.11) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage3 | East-African-Indian | CAS | RD750 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrB | 6742 | p.Glu501Asp | missense_variant | 0.7 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| gyrA | 7566 | p.Asp89Asn | missense_variant | 0.21 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| gyrA | 7572 | p.Ser91Pro | missense_variant | 0.11 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| pncA | 2288752 | p.Ser164Pro | missense_variant | 0.23 | pyrazinamide |
| pncA | 2288778 | p.Val155Gly | missense_variant | 0.65 | pyrazinamide |
| gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
| 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 |
| rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
| rpoC | 762434 | c.-936T>G | upstream_gene_variant | 1.0 |
| 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 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_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 | 2170342 | c.250_270delGAGCAGGCGGCCACCCAGGCC | conservative_inframe_deletion | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 |
| pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
| pncA | 2289787 | c.-546A>C | upstream_gene_variant | 1.0 |
| ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473820 | c.-187C>A | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| embC | 4240009 | c.147G>A | synonymous_variant | 1.0 |
| embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
