Run ID: ERR4797458
Sample name:
Date: 20-10-2023 02:19:28
Number of reads: 4016962
Percentage reads mapped: 99.66
Strain: lineage3
Drug-resistance: XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Asp435Val (1.00) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | ||
| Pyrazinamide | R | pncA p.Val139Met (1.00) |
| Streptomycin | ||
| Fluoroquinolones | R | gyrA p.Asp94Gly (1.00) |
| Moxifloxacin | R | gyrA p.Asp94Gly (1.00) |
| Ofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Levofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Ciprofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Aminoglycosides | R | rrs n.1401A>G (1.00) |
| Amikacin | R | rrs n.1401A>G (1.00) |
| Capreomycin | R | rrs n.1401A>G (1.00) |
| Kanamycin | R | rrs n.1401A>G (1.00) |
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | R | folC p.Ser150Gly (1.00) |
| Delamanid | ||
| Bedaquiline | ||
| Linezolid | R | rrl n.2814G>T (0.60) |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage3 | East-African-Indian | CAS | RD750 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761110 | p.Asp435Val | missense_variant | 1.0 | rifampicin |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
| rrl | 1476471 | n.2814G>T | non_coding_transcript_exon_variant | 0.6 | linezolid |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2288827 | p.Val139Met | missense_variant | 1.0 | pyrazinamide |
| folC | 2747151 | p.Ser150Gly | missense_variant | 1.0 | para-aminosalicylic_acid |
| 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 |
| fbiC | 1305366 | p.Met812Ile | missense_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrs | 1471926 | n.81C>T | non_coding_transcript_exon_variant | 1.0 |
| rrl | 1475927 | n.2270G>T | non_coding_transcript_exon_variant | 0.3 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| tlyA | 1918172 | p.Ala78Val | missense_variant | 1.0 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| katG | 2156008 | p.Asn35Thr | missense_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2289047 | c.195C>T | synonymous_variant | 0.99 |
| pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
| kasA | 2519092 | p.Ile326Met | missense_variant | 1.0 |
| ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| whiB7 | 3568857 | c.-178C>T | upstream_gene_variant | 1.0 |
| panD | 4044023 | c.259C>T | synonymous_variant | 1.0 |
| embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embB | 4248103 | c.1590G>A | synonymous_variant | 1.0 |
| ethA | 4327370 | p.Leu35Arg | missense_variant | 0.99 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
| gid | 4407871 | c.331delG | frameshift_variant | 1.0 |
