Run ID: ERR3014593
Sample name:
Date: 20-10-2023 21:32:00
Number of reads: 2976779
Percentage reads mapped: 99.5
Strain: lineage4.3.1
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.Pro62Leu (1.00) |
Streptomycin | ||
Fluoroquinolones | R | gyrB p.Asp461Asn (1.00), gyrA p.Asp94Ala (0.98) |
Moxifloxacin | R | gyrB p.Asp461Asn (1.00), gyrA p.Asp94Ala (0.98) |
Ofloxacin | R | gyrB p.Asp461Asn (1.00), gyrA p.Asp94Ala (0.98) |
Levofloxacin | R | gyrB p.Asp461Asn (1.00), gyrA p.Asp94Ala (0.98) |
Ciprofloxacin | R | gyrB p.Asp461Asn (1.00), gyrA p.Asp94Ala (0.98) |
Aminoglycosides | ||
Amikacin | R | eis c.-14C>T (0.98) |
Capreomycin | ||
Kanamycin | R | eis c.-14C>T (0.98) |
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (1.00), ethA c.106delG (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 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.1 | Euro-American (LAM) | LAM9 | None | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrB | 6620 | p.Asp461Asn | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Ala | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289057 | p.Pro62Leu | missense_variant | 1.0 | pyrazinamide |
eis | 2715346 | c.-14C>T | upstream_gene_variant | 0.98 | kanamycin, amikacin |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
ethA | 4327367 | c.106delG | frameshift_variant | 1.0 | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
rpoC | 766487 | p.Pro1040Ser | missense_variant | 0.18 |
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 | 1475317 | n.1660G>A | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102705 | c.330_337delCCCCTACG | frameshift_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087856 | p.His346Pro | missense_variant | 0.94 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338599 | c.-78A>C | upstream_gene_variant | 0.37 |
gid | 4408061 | p.His48Tyr | missense_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |