Run ID: ERR4811554
Sample name:
Date: 20-10-2023 00:49:41
Number of reads: 7034910
Percentage reads mapped: 99.22
Strain: lineage2.2.1.1;lineage2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.13) |
Isoniazid | R | katG p.Ser315Thr (0.15) |
Ethambutol | R | embB p.Met306Val (0.13) |
Pyrazinamide | R | pncA p.Asp12Ala (0.14) |
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 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.88 |
lineage2.1 | East-Asian (non-Beijing) | None | None | 0.14 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.88 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 0.86 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.13 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.15 | isoniazid |
pncA | 2289207 | p.Asp12Ala | missense_variant | 0.14 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.13 | ethambutol |
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 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.86 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.83 |
rpoB | 760281 | p.Thr159Pro | missense_variant | 0.13 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 765121 | c.1752G>A | synonymous_variant | 0.14 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.86 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.88 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1304443 | p.Ala505Thr | missense_variant | 0.14 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.85 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155506 | c.606C>A | synonymous_variant | 0.14 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyX | 3067713 | p.Val78Ala | missense_variant | 0.88 |
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 | 0.87 |
clpC1 | 4040841 | c.-138delG | upstream_gene_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.87 |
embB | 4246088 | c.-426A>G | upstream_gene_variant | 0.17 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
ethA | 4327392 | p.Pro28Ser | missense_variant | 0.86 |
whiB6 | 4338350 | p.Arg58Cys | missense_variant | 0.85 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
whiB6 | 4338675 | c.-154C>G | upstream_gene_variant | 0.83 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407766 | p.Thr146Arg | missense_variant | 0.14 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.86 |