Run ID: ERR2707080
Sample name:
Date: 19-10-2023 12:11:59
Number of reads: 3513782
Percentage reads mapped: 99.54
Strain: lineage4.1.1.1
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Leu452Pro (0.99) |
| Isoniazid | R | katG p.Ser315Asn (1.00) |
| Ethambutol | R | embB p.Met306Ile (1.00) |
| Pyrazinamide | ||
| Streptomycin | ||
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| 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 | R | ethA c.509dupA (1.00), ethA c.252_253dupCG (0.99), ethA c.946_1139del (1.00) |
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
| lineage4.1 | Euro-American | T;X;H | None | 1.0 |
| lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 1.0 |
| lineage4.1.1.1 | Euro-American (X-type) | X2 | RD183 | 0.95 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761161 | p.Leu452Pro | missense_variant | 0.99 | rifampicin |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
| katG | 2155168 | p.Ser315Asn | missense_variant | 1.0 | isoniazid |
| embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
| ethA | 4326964 | c.509dupA | frameshift_variant | 1.0 | ethionamide |
| ethA | 4327220 | c.252_253dupCG | frameshift_variant | 0.99 | ethionamide |
| ethA | 4326334 | c.946_1139del | frameshift_variant | 1.0 | ethionamide |
| 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 |
| rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrl | 1476055 | n.2398C>T | non_coding_transcript_exon_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| ahpC | 2726210 | c.18T>C | synonymous_variant | 0.99 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fbiD | 3339550 | p.Gly145Arg | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.98 |
| fbiA | 3641447 | p.Thr302Met | missense_variant | 0.99 |
| rpoA | 3877553 | p.Glu319Lys | missense_variant | 1.0 |
| embC | 4240897 | c.1035C>G | synonymous_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.99 |
| embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
| embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
