Run ID: SRR27107261
Sample name:
Date: 06-02-2024 05:50:40
Number of reads: 4536956
Percentage reads mapped: 99.53
Strain: lineage4.4.1.1
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.His445Cys (0.99) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.Met306Ile (0.99) |
| Pyrazinamide | R | pncA p.Cys72Tyr (1.00) |
| Streptomycin | R | gid c.351dupG (1.00) |
| Fluoroquinolones | R | gyrA p.Ala90Val (1.00) |
| Moxifloxacin | R | gyrA p.Ala90Val (1.00) |
| Ofloxacin | R | gyrA p.Ala90Val (1.00) |
| Levofloxacin | R | gyrA p.Ala90Val (1.00) |
| Ciprofloxacin | R | gyrA p.Ala90Val (1.00) |
| Aminoglycosides | ||
| Amikacin | R | eis c.-14C>T (1.00) |
| Capreomycin | ||
| Kanamycin | R | eis c.-14C>T (1.00) |
| Cycloserine | ||
| Ethionamide | R | ethA c.1265delC (1.00), ethA c.1265delC (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 |
| lineage4.4 | Euro-American | S;T | None | 1.0 |
| lineage4.4.1 | Euro-American (S-type) | S;T | None | 1.0 |
| lineage4.4.1.1 | Euro-American | S;Orphans | None | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761139 | p.His445Cys | missense_variant | 0.99 | rifampicin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2289027 | p.Cys72Tyr | missense_variant | 1.0 | pyrazinamide |
| eis | 2715346 | c.-14C>T | upstream_gene_variant | 1.0 | kanamycin, amikacin |
| embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | ethambutol |
| ethA | 4326208 | c.1265delC | frameshift_variant | 1.0 | ethionamide, ethionamide |
| gid | 4407851 | c.351dupG | frameshift_variant | 1.0 | streptomycin |
| 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 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| fbiC | 1302772 | c.-159T>C | upstream_gene_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| ndh | 2102990 | p.Val18Ala | missense_variant | 1.0 |
| PPE35 | 2169840 | p.Gly258Asp | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.99 |
| thyX | 3067949 | c.-4C>T | upstream_gene_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| ald | 3086844 | c.27delC | frameshift_variant | 1.0 |
| Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| Rv3236c | 3612665 | p.Val151Ala | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embB | 4247122 | c.609G>A | synonymous_variant | 1.0 |
| ethA | 4327740 | c.-267A>G | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
