Run ID: ERR2516555
Sample name:
Date: 19-10-2023 23:41:47
Number of reads: 3750782
Percentage reads mapped: 99.5
Strain: lineage4.1
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Asp435Gly (0.99), rpoB p.Arg448Gln (1.00) |
| Isoniazid | R | katG c.2002dupT (0.99), katG c.2002dupT (0.99), ahpC c.-52C>T (1.00) |
| Ethambutol | R | embB p.Met306Ile (1.00) |
| Pyrazinamide | R | pncA c.14_*617del (1.00) |
| Streptomycin | ||
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | ethA p.Ala341Val (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 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761110 | p.Asp435Gly | missense_variant | 0.99 | rifampicin |
| rpoB | 761149 | p.Arg448Gln | missense_variant | 1.0 | rifampicin |
| katG | 2154109 | c.2002dupT | frameshift_variant | 0.99 | isoniazid, isoniazid |
| ahpC | 2726141 | c.-52C>T | upstream_gene_variant | 1.0 | isoniazid |
| embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
| ethA | 4326452 | p.Ala341Val | missense_variant | 1.0 | ethionamide |
| pncA | 2288063 | c.14_*617del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | pyrazinamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 8694 | c.1393C>T | synonymous_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| rpoC | 764613 | p.Gln415Arg | 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 |
| rrs | 1473306 | n.1461A>G | non_coding_transcript_exon_variant | 1.0 |
| rpsA | 1834348 | c.807T>C | synonymous_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| katG | 2154676 | p.Ala479Gly | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3449738 | p.His412Arg | missense_variant | 0.96 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| fprA | 3475346 | p.Leu447Arg | missense_variant | 1.0 |
| Rv3236c | 3612515 | p.Arg201His | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| 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 |
| gid | 4408031 | p.Leu58Phe | missense_variant | 1.0 |
| whiB6 | 4337987 | c.271_*183del | stop_lost&conservative_inframe_deletion&splice_region_variant | 0.98 |
