Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1849 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0228555399 sf0228549530 2 28555399 1.53E-08 8.05E-07
vg0803532222 sf0803531225 8 3532222 1.94E-08 2.44E-07
vg1214958039 sf1214955381 12 14958039 6.27E-08 7.58E-07
vg0906306952 sf0906305952 9 6306952 9.21E-08 8.01E-07
vg1215048657 sf1215045999 12 15048657 2.60E-07 4.32E-06
vg0412664006 sf0412654716 4 12664006 3.03E-07 3.43E-06
vg0921539163 sf0921538682 9 21539163 9.96E-07 8.02E-08
vg1115925850 sf1115460720 11 15925850 1.03E-06 1.39E-06
vg0815304114 sf0815301400 8 15304114 2.32E-06 1.82E-06
vg1208634025 sf1208631432 12 8634025 5.29E-06 4.06E-06
vg1214703763 sf1214701104 12 14703763 6.67E-06 3.52E-07
vg1215013173 sf1215010515 12 15013173 NA 3.00E-08
vg0916030541 sf0916029540 9 16030541 NA 3.96E-07
vg0315388478 sf0315387125 3 15388478 NA 4.01E-07
vg0823650185 sf0823647471 8 23650185 NA 6.41E-07
vg0207745017 sf0207745016 2 7745017 NA 8.72E-07
vg1122942389 sf1122476260 11 22942389 NA 1.05E-06
vg0401719938 sf0401715487 4 1719938 NA 1.43E-06
vg0820029176 sf0820026463 8 20029176 NA 3.11E-06