Run ID: ERR7911413
Sample name:
Date: 19-10-2023 13:14:09
Number of reads: 4685097
Percentage reads mapped: 99.8
Strain: lineage4.8;lineage4.3.3
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | R | katG p.Ser315Thr (0.71) |
Ethambutol | ||
Pyrazinamide | ||
Streptomycin | ||
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
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 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.25 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 0.73 |
lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 0.27 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 0.71 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.4 |
gyrA | 8040 | p.Gly247Ser | missense_variant | 0.33 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.25 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.23 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.25 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303095 | c.165G>A | synonymous_variant | 0.2 |
fbiC | 1303106 | p.Cys59Tyr | missense_variant | 0.8 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.51 |
rpsA | 1834836 | p.Met432Thr | missense_variant | 0.26 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2156196 | c.-85C>T | upstream_gene_variant | 0.27 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.71 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.23 |
folC | 2746340 | p.Ala420Val | missense_variant | 0.17 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.27 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.26 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.32 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.16 |
clpC1 | 4038968 | c.1737G>A | synonymous_variant | 0.27 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.31 |