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 mr1102 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
vg0922486625 sf0922486144 9 22486625 2.21E-24 NA
vg0626494211 sf0626493214 6 26494211 6.94E-24 NA
vg0800427985 sf0800426985 8 427985 7.23E-24 NA
vg1013262010 sf1013190780 10 13262010 9.02E-24 NA
vg0907770893 sf0907769893 9 7770893 1.81E-23 NA
vg0819251922 sf0819249209 8 19251922 1.01E-22 4.07E-06
vg0220102123 sf0220096255 2 20102123 NA 1.48E-06
vg0321403368 sf0321401878 3 21403368 NA 2.05E-06
vg0626320718 sf0626319721 6 26320718 NA 4.99E-06