Run ID: SRR847803
Sample name:
Date: 21-10-2023 00:34:46
Number of reads: 7408218
Percentage reads mapped: 99.53
Strain: lineage4.1.1.3
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.Phe330Val (1.00) |
Pyrazinamide | R | pncA p.Asp12Ala (1.00) |
Streptomycin | ||
Fluoroquinolones | R | gyrA p.Ser91Pro (1.00) |
Moxifloxacin | R | gyrA p.Ser91Pro (1.00) |
Ofloxacin | R | gyrA p.Ser91Pro (1.00) |
Levofloxacin | R | gyrA p.Ser91Pro (1.00) |
Ciprofloxacin | R | gyrA p.Ser91Pro (1.00) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | R | tlyA c.735_744delGCAGACCGAC (1.00), tlyA c.735_744delGCAGACCGAC (1.00) |
Kanamycin | ||
Cycloserine | R | ald c.134_135dupTC (1.00) |
Ethionamide | R | ethA c.-692_*1293del (1.00) |
Clofazimine | ||
Para-aminosalicylic_acid | R | thyX c.-16C>T (1.00), thyA c.-4081_*1079del (1.00) |
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 | 7572 | p.Ser91Pro | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
tlyA | 1918671 | c.735_744delGCAGACCGAC | frameshift_variant | 1.0 | capreomycin, capreomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289207 | p.Asp12Ala | missense_variant | 1.0 | pyrazinamide |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid |
ald | 3086952 | c.134_135dupTC | frameshift_variant | 1.0 | cycloserine |
embB | 4247501 | p.Phe330Val | missense_variant | 1.0 | ethambutol |
thyA | 3072600 | c.-4081_*1079del | transcript_ablation | 1.0 | para-aminosalicylic_acid |
ethA | 4324710 | c.-692_*1293del | transcript_ablation | 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 | 763555 | c.186C>T | synonymous_variant | 1.0 |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
rpoC | 766744 | p.Gln1125His | missense_variant | 1.0 |
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 |
rpsA | 1834023 | p.Leu161Gln | missense_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449494 | p.Cys331Arg | missense_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
clpC1 | 4038649 | p.Gly686Ser | missense_variant | 1.0 |
embC | 4239763 | c.-100C>T | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embC | 4242803 | p.Val981Leu | missense_variant | 0.99 |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
ubiA | 4269296 | p.Met180Val | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407790 | p.Ala138Val | missense_variant | 1.0 |