Run ID: ERR2510683
Sample name:
Date: 20-10-2023 06:26:20
Number of reads: 3658360
Percentage reads mapped: 96.53
Strain: lineage4.1.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Glu405Asp (1.00) |
Pyrazinamide | ||
Streptomycin | R | rpsL p.Lys88Gln (1.00) |
Fluoroquinolones | R | gyrA p.Asp94Tyr (1.00) |
Moxifloxacin | R | gyrA p.Asp94Tyr (1.00) |
Ofloxacin | R | gyrA p.Asp94Tyr (1.00) |
Levofloxacin | R | gyrA p.Asp94Tyr (1.00) |
Ciprofloxacin | R | gyrA p.Asp94Tyr (1.00) |
Aminoglycosides | R | rrs n.1402C>T (1.00) |
Amikacin | R | rrs n.1402C>T (1.00) |
Capreomycin | R | rrs n.1402C>T (1.00) |
Kanamycin | R | rrs n.1402C>T (1.00) |
Cycloserine | ||
Ethionamide | ||
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 |
lineage4.1.2 | Euro-American | T;H | None | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Tyr | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781821 | p.Lys88Gln | missense_variant | 1.0 | streptomycin |
rrs | 1473247 | n.1402C>T | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
embB | 4247728 | p.Glu405Asp | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7323 | p.Pro8Ala | missense_variant | 1.0 |
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 | 1.0 |
rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 766488 | p.Pro1040Arg | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776659 | p.Asp608Asn | 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 |
PPE35 | 2168501 | p.Phe704Leu | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518076 | c.-39C>T | 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 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
embB | 4247121 | p.Ser203Leu | missense_variant | 1.0 |
ubiA | 4269088 | p.Ala249Val | missense_variant | 1.0 |
ubiA | 4269341 | p.Gly165Ser | missense_variant | 1.0 |
ethA | 4327307 | p.Asp56Ala | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |