Run ID: ERR9806978
Sample name:
Date: 21-05-2023 06:41:30
Number of reads: 2774704
Percentage reads mapped: 99.55
Strain: lineage4.1.1.3
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Met306Ile (1.00) |
Pyrazinamide | R | pncA p.Ser164Pro (1.00) |
Streptomycin | R | rpsL p.Lys43Arg (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 | R | rrs n.1401A>G (1.00) |
Amikacin | R | rrs n.1401A>G (1.00) |
Capreomycin | R | rrs n.1401A>G (1.00) |
Kanamycin | R | rrs n.1401A>G (1.00) |
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (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 |
lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 1.0 |
lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 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 |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288752 | p.Ser164Pro | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
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 |
gyrA | 9416 | c.2115C>T | synonymous_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 |
rpsL | 781435 | c.-125G>C | upstream_gene_variant | 1.0 |
fbiC | 1303087 | p.Asp53Asn | missense_variant | 1.0 |
embR | 1416606 | p.Arg248Cys | missense_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2222133 | c.1031delA | frameshift_variant | 0.14 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568604 | c.75delC | frameshift_variant | 0.12 |
fbiA | 3640747 | p.Leu69Met | missense_variant | 0.12 |
fbiB | 3642055 | p.Arg174His | missense_variant | 0.14 |
alr | 3841593 | c.-173C>T | upstream_gene_variant | 1.0 |
rpoA | 3878496 | c.12A>G | synonymous_variant | 0.14 |
embA | 4242298 | c.-935C>T | upstream_gene_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embA | 4243512 | p.Pro94Ser | missense_variant | 0.11 |
embA | 4243812 | c.580C>A | synonymous_variant | 0.12 |
embB | 4247138 | c.625C>A | synonymous_variant | 0.11 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
ethA | 4326123 | p.Ser451Pro | missense_variant | 1.0 |
ethA | 4328449 | c.-976C>T | upstream_gene_variant | 0.11 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407798 | c.405G>T | synonymous_variant | 1.0 |