Run ID: ERR2515622
Sample name:
Date: 20-10-2023 14:10:04
Number of reads: 1139404
Percentage reads mapped: 99.76
Strain: lineage4.3.3;lineage4.3.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Asp435Gly (0.59), rpoB p.Leu452Pro (0.57) |
Isoniazid | R | fabG1 c.-8T>A (0.63), katG p.Ser315Thr (0.57) |
Ethambutol | R | embB p.Met306Val (0.60) |
Pyrazinamide | R | pncA c.456dupC (0.52), pncA c.456dupC (0.52) |
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Ala90Val (0.40) |
Moxifloxacin | R | gyrA p.Ala90Val (0.40) |
Ofloxacin | R | gyrA p.Ala90Val (0.40) |
Levofloxacin | R | gyrA p.Ala90Val (0.40) |
Ciprofloxacin | R | gyrA p.Ala90Val (0.40) |
Aminoglycosides | R | rrs n.1401A>G (0.71) |
Amikacin | R | rrs n.1401A>G (0.71) |
Capreomycin | R | rrs n.1401A>G (0.71) |
Kanamycin | R | rrs n.1401A>G (0.71) |
Cycloserine | ||
Ethionamide | R | ethA c.-11A>G (0.57) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.2 | Euro-American (LAM) | LAM3 | None | 0.39 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 0.64 |
lineage4.3.2.1 | Euro-American (LAM) | LAM3 | RD761 | 0.42 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.4 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761110 | p.Asp435Gly | missense_variant | 0.59 | rifampicin |
rpoB | 761161 | p.Leu452Pro | missense_variant | 0.57 | rifampicin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.71 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673432 | c.-8T>A | upstream_gene_variant | 0.63 | isoniazid |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.57 | isoniazid |
pncA | 2288785 | c.456dupC | frameshift_variant | 0.52 | pyrazinamide, pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.6 | ethambutol |
ethA | 4327484 | c.-11A>G | upstream_gene_variant | 0.57 | ethionamide |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5520 | p.Pro94Leu | missense_variant | 0.34 |
gyrA | 7222 | c.-80C>T | upstream_gene_variant | 0.42 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 0.97 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 0.68 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoB | 763123 | p.Ile1106Thr | missense_variant | 0.61 |
rpoC | 764995 | c.1626C>G | synonymous_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 | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476056 | n.2399G>A | non_coding_transcript_exon_variant | 0.58 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223051 | p.Glu38Asp | missense_variant | 0.61 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.54 |
Rv2752c | 3065824 | p.Pro123Leu | missense_variant | 0.53 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.97 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
clpC1 | 4039937 | c.768G>T | synonymous_variant | 0.34 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
ubiA | 4269271 | p.Val188Ala | missense_variant | 0.61 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |