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 mr1258 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
vg1006193277 sf1006208926 10 6193277 2.19E-12 6.66E-10
vg1007771968 sf1007787578 10 7771968 5.01E-12 2.91E-10
vg1008991063 sf1008919924 10 8991063 2.87E-11 1.76E-09
vg1006124926 sf1006141462 10 6124926 5.59E-11 2.99E-10
vg1204314449 sf1204313437 12 4314449 1.50E-10 7.95E-09
vg0407825687 sf0407820955 4 7825687 1.06E-09 2.46E-07
vg0407825479 sf0407820747 4 7825479 1.31E-09 1.81E-07
vg1216843191 sf1216837145 12 16843191 2.76E-09 1.28E-07
vg0403205033 sf0403200636 4 3205033 2.88E-09 5.20E-07
vg0716828450 sf0716827457 7 16828450 2.04E-08 2.40E-07
vg1006521377 sf1006537000 10 6521377 3.78E-08 1.73E-06
vg0528415027 sf0528352382 5 28415027 3.99E-08 3.91E-06
vg1010574400 sf1010503221 10 10574400 2.09E-07 4.03E-07
vg1105156994 sf1105152805 11 5156994 1.93E-06 4.64E-06
vg0403206782 sf0403202385 4 3206782 7.65E-06 3.69E-07
vg1216422805 sf1216420098 12 16422805 NA 2.68E-06