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 mr1961 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
vg0819897831 sf0819895118 8 19897831 9.97E-09 8.73E-07
vg0335766881 sf0335759750 3 35766881 2.27E-08 3.57E-06
vg0819850762 sf0819848049 8 19850762 1.10E-07 4.72E-07
vg0504420610 sf0504420587 5 4420610 2.32E-07 8.00E-07
vg1210377244 sf1210374657 12 10377244 3.32E-07 3.04E-07
vg0909369883 sf0909368882 9 9369883 7.12E-07 3.80E-06
vg0911337326 sf0911336325 9 11337326 1.00E-06 4.03E-06
vg1009711911 sf1009640732 10 9711911 1.93E-06 2.45E-06
vg0312486433 sf0312485151 3 12486433 5.43E-06 4.07E-06