Run ID: ERR4813742
Sample name:
Date: 20-10-2023 16:20:33
Number of reads: 1269171
Percentage reads mapped: 99.63
Strain: lineage4.3.4.1;lineage4.1.2.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | R | fabG1 c.-15C>T (0.22) |
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | ||
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (0.22) |
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 | 0.38 |
lineage4.1 | Euro-American | T;X;H | None | 0.65 |
lineage4.1.2 | Euro-American | T;H | None | 0.63 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 0.34 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.64 |
lineage4.3.4.1 | Euro-American (LAM) | LAM1;LAM2 | RD174 | 0.36 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.22 | isoniazid, 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 | 8715 | p.Pro472Ser | missense_variant | 0.28 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.73 |
mshA | 575679 | p.Asn111Ser | missense_variant | 0.62 |
rpoB | 759608 | c.-199C>T | upstream_gene_variant | 0.39 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.71 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.36 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.48 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1407489 | c.-149G>A | upstream_gene_variant | 0.64 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.65 |
ahpC | 2726323 | p.Pro44Arg | missense_variant | 0.26 |
pepQ | 2859830 | p.Gly197Arg | missense_variant | 0.43 |
Rv2752c | 3066299 | c.-108C>T | upstream_gene_variant | 0.67 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3448598 | p.Ile32Thr | missense_variant | 0.5 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612768 | p.Ala117Pro | missense_variant | 0.32 |
fbiB | 3641208 | c.-327C>T | upstream_gene_variant | 0.6 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.37 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.64 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.44 |