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 mr1763 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
vg0722226606 sf0722225613 7 22226606 5.22E-08 NA
vg1011333524 sf1011262344 10 11333524 8.43E-08 NA
vg0324965295 sf0324963375 3 24965295 2.22E-07 5.04E-06
vg1007607743 sf1007623352 10 7607743 2.29E-07 2.83E-06
vg0519574921 sf0519512405 5 19574921 4.94E-07 3.37E-06
vg0613979134 sf0613978135 6 13979134 1.97E-06 2.88E-06
vg0431894926 sf0431709821 4 31894926 2.36E-06 NA