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 mr1289 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
vg0103243562 sf0103242562 1 3243562 1.08E-08 8.19E-06
vg0103243306 sf0103242306 1 3243306 1.78E-08 5.82E-06
vg1210333120 sf1210330533 12 10333120 3.73E-08 NA
vg1011427851 sf1011356670 10 11427851 6.02E-08 NA
vg0315003502 sf0315002149 3 15003502 9.74E-08 NA
vg0315008841 sf0315007488 3 15008841 1.03E-06 NA
vg0208995146 sf0208995144 2 8995146 7.40E-06 NA