Run ID: ERR4817295
Sample name:
Date: 20-10-2023 08:21:06
Number of reads: 2293094
Percentage reads mapped: 99.58
Strain: lineage4.2.2.2;lineage2.2.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | R | katG p.Ser315Thr (0.58) |
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 |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.5 |
lineage4 | Euro-American | LAM;T;S;X;H | None | 0.46 |
lineage4.2 | Euro-American | H;T;LAM | None | 0.53 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.52 |
lineage4.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.49 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.47 |
lineage4.2.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.55 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 0.58 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8688 | p.Ala463Ser | missense_variant | 0.42 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.54 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.67 |
mshA | 576077 | c.730C>T | synonymous_variant | 0.45 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.54 |
rpoB | 761489 | c.1683G>A | synonymous_variant | 0.58 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.46 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.4 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.51 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.43 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.48 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.53 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.57 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.48 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2714526 | c.805_806delAC | frameshift_variant | 0.35 |
Rv2752c | 3065711 | p.Gly161Ser | missense_variant | 0.62 |
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 0.46 |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.46 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.54 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.66 |
embB | 4248006 | p.Thr498Asn | missense_variant | 0.45 |
embB | 4248375 | p.Trp621Ser | missense_variant | 0.54 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.5 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.42 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.42 |