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 mr1971 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
vg0611065547 sf0611064548 6 11065547 8.52E-12 8.52E-12
vg0611061199 sf0611060200 6 11061199 1.11E-11 1.11E-11
vg0614795778 sf0614794779 6 14795778 1.53E-08 1.53E-08
vg0617382754 sf0617381757 6 17382754 4.88E-08 4.88E-08
vg0620630387 sf0620629390 6 20630387 8.41E-08 8.41E-08
vg0611102764 sf0611101765 6 11102764 1.69E-06 1.69E-06
vg0102103893 sf0102102893 1 2103893 2.95E-06 2.95E-06
vg0620202115 sf0620201118 6 20202115 3.26E-06 3.26E-06
vg0400559351 sf0400558351 4 559351 4.30E-06 4.30E-06