Run ID: ERR11488482
Sample name:
Date: 06-01-2024 19:35:45
Number of reads: 3990750
Percentage reads mapped: 99.56
Strain: lineage4.1.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.98) |
Isoniazid | R | katG p.Ser315Thr (1.00), ahpC c.-57C>T (0.96) |
Ethambutol | R | embB p.Asp1024Asn (0.96) |
Pyrazinamide | R | pncA p.Thr135Pro (0.96) |
Streptomycin | R | rpsL p.Lys43Arg (1.00) |
Fluoroquinolones | R | gyrA p.Asp94Ala (0.90) |
Moxifloxacin | R | gyrA p.Asp94Ala (0.90) |
Ofloxacin | R | gyrA p.Asp94Ala (0.90) |
Levofloxacin | R | gyrA p.Asp94Ala (0.90) |
Ciprofloxacin | R | gyrA p.Asp94Ala (0.90) |
Aminoglycosides | R | rrs n.1401A>G (0.94) |
Amikacin | R | rrs n.1401A>G (0.94) |
Capreomycin | R | rrs n.1401A>G (0.94) |
Kanamycin | R | rrs n.1401A>G (0.94) |
Cycloserine | ||
Ethionamide | R | ethA c.860delA (0.93), ethA c.860delA (0.93) |
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 | 0.97 |
lineage4.1.2 | Euro-American | T;H | None | 0.96 |
lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 0.94 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | missense_variant | 0.9 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.98 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.94 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288839 | p.Thr135Pro | missense_variant | 0.96 | pyrazinamide |
ahpC | 2726136 | c.-57C>T | upstream_gene_variant | 0.96 | isoniazid |
embB | 4249583 | p.Asp1024Asn | missense_variant | 0.96 | ethambutol |
ethA | 4326613 | c.860delA | frameshift_variant | 0.93 | ethionamide, 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 |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.94 |
mshA | 575679 | p.Asn111Ser | missense_variant | 0.94 |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.98 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.94 |
rpoC | 766488 | p.Pro1040Arg | missense_variant | 0.96 |
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 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2101847 | p.Leu399Arg | missense_variant | 0.84 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.94 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.95 |
embB | 4247503 | p.Phe330Leu | missense_variant | 0.96 |
ubiA | 4269308 | p.Phe176Leu | missense_variant | 0.95 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338635 | c.-114A>C | upstream_gene_variant | 0.94 |