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 mr1981 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
vg0630078359 sf0630077361 6 30078359 2.17E-08 4.22E-06
vg1219157807 sf1219129241 12 19157807 5.22E-08 NA
vg1104258287 sf1104254189 11 4258287 1.05E-07 8.71E-07
vg1104258278 sf1104254180 11 4258278 1.07E-07 8.81E-07
vg0622395868 sf0622394871 6 22395868 2.11E-07 NA
vg0206101217 sf0206101217 2 6101217 4.08E-07 NA
vg1104591250 sf1104587152 11 4591250 7.97E-07 1.74E-06