Run ID: SRR25827693
Sample name:
Date: 02-02-2024 15:09:21
Number of reads: 6219743
Percentage reads mapped: 98.86
Strain: lineage3;lineage2.2.1.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00) |
Isoniazid | R | katG p.Ser315Thr (0.26) |
Ethambutol | R | embB p.Met306Val (0.35) |
Pyrazinamide | R | pncA p.Ala146Thr (0.31) |
Streptomycin | R | rpsL p.Lys43Arg (0.26) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | ||
Clofazimine | ||
Para-aminosalicylic_acid | ||
Delamanid | ||
Bedaquiline | ||
Linezolid |
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage3 | East-African-Indian | CAS | RD750 | 0.68 |
lineage2 | East-Asian | Beijing | RD105 | 0.31 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.29 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.31 |
lineage2.2.1.1 | East-Asian (Beijing) | Beijing-RD150 | RD105;RD207;RD181;RD150 | 0.32 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.26 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.26 | isoniazid |
pncA | 2288806 | p.Ala146Thr | missense_variant | 0.31 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.35 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5052 | c.-188A>G | upstream_gene_variant | 0.67 |
gyrB | 6737 | p.Thr500Ala | missense_variant | 0.24 |
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 | 0.36 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.34 |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.75 |
rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.68 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764363 | p.Gly332Ser | missense_variant | 0.39 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.31 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.29 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781879 | p.Val107Ala | missense_variant | 0.71 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.32 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.3 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.68 |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.73 |
eis | 2714846 | p.Val163Ile | missense_variant | 0.33 |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.73 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612563 | p.Met185Thr | missense_variant | 0.69 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.33 |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.62 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.24 |
embB | 4247880 | p.Val456Ala | missense_variant | 0.3 |
embB | 4248115 | c.1602C>T | synonymous_variant | 0.28 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.32 |
ethA | 4328437 | c.-965dupC | upstream_gene_variant | 0.28 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.32 |