Run ID: ERR4798603
Sample name:
Date: 20-10-2023 03:03:18
Number of reads: 4367335
Percentage reads mapped: 99.49
Strain: lineage1.1.2
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (0.99) |
| Isoniazid | R | fabG1 c.-15C>T (1.00) |
| Ethambutol | R | embA c.-12C>T (1.00) |
| Pyrazinamide | ||
| Streptomycin | R | gid c.102delG (1.00) |
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-15C>T (1.00) |
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage1 | Indo-Oceanic | EAI | RD239 | 1.0 |
| lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 1.0 |
| lineage1.1.2 | Indo-Oceanic | EAI3;EAI5 | RD239 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
| embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol |
| gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
| gyrB | 6124 | c.885C>T | synonymous_variant | 1.0 |
| gyrB | 6902 | p.Leu555Val | missense_variant | 0.94 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 |
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| rpoB | 760130 | c.324T>C | synonymous_variant | 1.0 |
| rpoB | 760490 | c.684C>T | synonymous_variant | 1.0 |
| rpoB | 760995 | c.1189C>A | synonymous_variant | 0.99 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
| rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 |
| rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 |
| rpoC | 765171 | p.Pro601Leu | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
| mmpL5 | 776395 | p.Phe696Leu | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| inhA | 1674682 | p.Met161Val | missense_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| ndh | 2101869 | p.Ala392Thr | missense_variant | 1.0 |
| ndh | 2101955 | p.Gln363Ser | missense_variant | 1.0 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| PPE35 | 2167701 | p.Ala971Gly | missense_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.97 |
| 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 | 1.0 |
| ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.99 |
| pepQ | 2860262 | p.Val53Met | missense_variant | 1.0 |
| Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
| fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
| clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 |
| embC | 4239952 | c.90G>A | synonymous_variant | 1.0 |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 |
| embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4243848 | p.Val206Met | missense_variant | 0.99 |
| embA | 4245218 | c.1986C>T | synonymous_variant | 0.99 |
| embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 |
| ubiA | 4269031 | p.Gly268Asp | missense_variant | 0.99 |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
| aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.99 |
| ethA | 4326650 | p.Gly275Glu | missense_variant | 0.96 |
| ethA | 4326906 | p.Leu190Phe | missense_variant | 0.99 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
| gid | 4407873 | c.330G>T | synonymous_variant | 0.99 |
