Run ID: SRR1166328
Sample name:
Date: 21-10-2023 10:24:19
Number of reads: 10799697
Percentage reads mapped: 99.58
Strain: lineage4.8
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00) |
| Isoniazid | R | katG p.Ser315Thr (0.99) |
| Ethambutol | R | embA c.-16C>T (1.00), embB p.Met306Val (1.00) |
| Pyrazinamide | R | pncA c.85dupC (1.00) |
| Streptomycin | R | rrs n.514A>C (1.00) |
| Fluoroquinolones | R | gyrA p.Asp94Ala (1.00) |
| Moxifloxacin | R | gyrA p.Asp94Ala (1.00) |
| Ofloxacin | R | gyrA p.Asp94Ala (1.00) |
| Levofloxacin | R | gyrA p.Asp94Ala (1.00) |
| Ciprofloxacin | R | gyrA p.Asp94Ala (1.00) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | R | eis c.-37G>T (1.00) |
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
| lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 1.0 | streptomycin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid |
| pncA | 2289156 | c.85dupC | frameshift_variant | 1.0 | pyrazinamide |
| eis | 2715369 | c.-37G>T | upstream_gene_variant | 1.0 | kanamycin |
| embA | 4243217 | c.-16C>T | upstream_gene_variant | 1.0 | ethambutol |
| embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| rpoC | 766487 | p.Pro1040Ser | 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 | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| Rv2752c | 3064515 | c.1677A>C | stop_lost&splice_region_variant | 1.0 |
| ald | 3087228 | p.Ala137Thr | missense_variant | 1.0 |
| Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embB | 4248694 | c.2181G>A | synonymous_variant | 1.0 |
| ethA | 4327052 | p.Tyr141Cys | missense_variant | 1.0 |
| ethR | 4327974 | p.Met142Ile | missense_variant | 0.99 |
| ethR | 4327975 | p.Gln143Lys | missense_variant | 1.0 |
| whiB6 | 4338269 | c.252delA | frameshift_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |
