Run ID: SRR671862
Sample name:
Date: 20-10-2023 21:50:38
Number of reads: 6117594
Percentage reads mapped: 99.48
Strain: lineage4.4.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Asn (0.98) |
Ethambutol | R | embA c.-11C>A (0.98) |
Pyrazinamide | R | pncA c.282_*290del (0.99) |
Streptomycin | R | gid p.Lys163* (0.99) |
Fluoroquinolones | R | gyrA p.Asp89Asn (0.16), gyrA p.Asp94Gly (0.84) |
Moxifloxacin | R | gyrA p.Asp89Asn (0.16), gyrA p.Asp94Gly (0.84) |
Ofloxacin | R | gyrA p.Asp89Asn (0.16), gyrA p.Asp94Gly (0.84) |
Levofloxacin | R | gyrA p.Asp89Asn (0.16), gyrA p.Asp94Gly (0.84) |
Ciprofloxacin | R | gyrA p.Asp89Asn (0.16), gyrA p.Asp94Gly (0.84) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
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 |
lineage4.4 | Euro-American | S;T | None | 1.0 |
lineage4.4.2 | Euro-American | T1;T2 | None | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7566 | p.Asp89Asn | missense_variant | 0.16 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.84 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Asn | missense_variant | 0.98 | isoniazid |
embA | 4243222 | c.-11C>A | upstream_gene_variant | 0.98 | ethambutol |
gid | 4407716 | p.Lys163* | stop_gained | 0.99 | streptomycin |
pncA | 2288390 | c.282_*290del | frameshift_variant&stop_lost&splice_region_variant | 0.99 | pyrazinamide |
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 |
mshA | 575503 | c.156G>A | synonymous_variant | 0.99 |
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 | 2102365 | c.678A>C | synonymous_variant | 0.97 |
katG | 2156484 | c.-373A>G | upstream_gene_variant | 1.0 |
PPE35 | 2169411 | c.1201dupA | frameshift_variant | 0.96 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
Rv2752c | 3066099 | p.Met31Ile | missense_variant | 0.98 |
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 |
embA | 4244329 | p.Ala366Glu | missense_variant | 0.99 |
embB | 4246508 | c.-6G>A | upstream_gene_variant | 0.99 |
embB | 4248026 | p.Ala505Thr | missense_variant | 0.73 |
aftB | 4267512 | p.Leu442His | missense_variant | 0.98 |
aftB | 4268928 | c.-92C>T | upstream_gene_variant | 1.0 |
aftB | 4269375 | c.-539G>A | upstream_gene_variant | 0.97 |
ethA | 4326977 | p.His166Pro | missense_variant | 0.99 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |