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 mr1162 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
vg0719981901 sf0719980908 7 19981901 2.07E-07 2.07E-07
vg1112898481 sf1112434802 11 12898481 5.62E-07 5.62E-07
vg0500172475 sf0500172475 5 172475 1.04E-06 1.04E-06
vg1200474744 sf1200473744 12 474744 1.94E-06 1.94E-06
vg1117514629 sf1117048484 11 17514629 2.01E-06 2.01E-06
vg1216729892 sf1216723846 12 16729892 2.40E-06 2.40E-06
vg0307151544 sf0307150542 3 7151544 4.65E-06 4.65E-06
vg1121750233 sf1121284110 11 21750233 7.95E-06 7.95E-06