Run ID: ERR10610231
Sample name:
Date: 22-05-2023 23:25:19
Number of reads: 2803631
Percentage reads mapped: 99.23
Strain: lineage1.2.2.1
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Asp435Val (0.98) |
| Isoniazid | R | fabG1 c.-15C>T (1.00), inhA p.Ser94Ala (0.97) |
| Ethambutol | ||
| Pyrazinamide | ||
| Streptomycin | R | rpsL p.Lys43Arg (0.98) |
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-15C>T (1.00), inhA p.Ser94Ala (0.97) |
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage1 | Indo-Oceanic | EAI | RD239 | 0.99 |
| lineage1.2.2 | Indo-Oceanic | EAI1 | RD239 | 0.99 |
| lineage1.2.2.1 | Indo-Oceanic | NA | RD239 | 0.98 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761110 | p.Asp435Val | missense_variant | 0.98 | rifampicin |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 0.98 | streptomycin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
| inhA | 1674481 | p.Ser94Ala | missense_variant | 0.97 | isoniazid, ethionamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 |
| gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 8452 | p.Ala384Val | missense_variant | 0.97 |
| gyrA | 9143 | c.1842T>C | synonymous_variant | 0.99 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| fgd1 | 491060 | p.Met93Thr | missense_variant | 1.0 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 0.99 |
| ccsA | 620659 | p.Arg257Cys | missense_variant | 0.99 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.99 |
| rpoC | 763884 | p.Ala172Val | missense_variant | 0.99 |
| rpoC | 763886 | c.517C>A | synonymous_variant | 0.99 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
| mmpL5 | 776698 | p.Pro595Ser | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| rplC | 800899 | p.Ala31Thr | missense_variant | 1.0 |
| Rv1258c | 1407264 | p.Ser26Leu | missense_variant | 1.0 |
| embR | 1417019 | p.Cys110Tyr | missense_variant | 0.96 |
| embR | 1417108 | c.240T>C | synonymous_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrs | 1471842 | n.-4T>G | upstream_gene_variant | 0.96 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 0.99 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| kasA | 2518132 | c.18C>T | synonymous_variant | 0.99 |
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 |
| Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.99 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fprA | 3474043 | p.Pro13Ser | missense_variant | 1.0 |
| fprA | 3474597 | c.591C>A | synonymous_variant | 0.98 |
| fprA | 3475159 | p.Asn385Asp | missense_variant | 0.99 |
| Rv3236c | 3612161 | p.Ala319Val | missense_variant | 0.98 |
| clpC1 | 4040212 | p.Pro165Ser | missense_variant | 1.0 |
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
| embC | 4239746 | c.-117C>G | upstream_gene_variant | 0.96 |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
| embC | 4240750 | c.888C>T | synonymous_variant | 1.0 |
| embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4245969 | p.Pro913Ser | missense_variant | 0.99 |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
| embB | 4248035 | p.Val508Phe | missense_variant | 1.0 |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.99 |
| ubiA | 4269896 | c.-63G>A | upstream_gene_variant | 0.98 |
| ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 |
| ethR | 4327450 | c.-99G>A | upstream_gene_variant | 0.98 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.98 |
| gid | 4407588 | c.615A>G | synonymous_variant | 0.99 |
| gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |
