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 mr1697 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
vg0810737306 sf0810736311 8 10737306 2.69E-11 4.56E-08
vg0814654076 sf0814651362 8 14654076 2.69E-11 4.56E-08
vg0313930936 sf0313929653 3 13930936 6.27E-11 1.40E-06
vg0710562047 sf0710561053 7 10562047 1.47E-10 2.56E-08
vg0815303600 sf0815300886 8 15303600 6.33E-10 4.23E-08
vg0824181264 sf0824178550 8 24181264 1.02E-09 8.99E-08
vg0324385736 sf0324383815 3 24385736 2.21E-09 1.12E-06
vg0401702306 sf0401697855 4 1702306 2.68E-09 1.92E-06
vg0519953159 sf0519890635 5 19953159 3.65E-09 9.05E-07
vg0511944956 sf0511944886 5 11944956 7.83E-09 2.82E-07
vg0804722355 sf0804721358 8 4722355 5.51E-08 2.82E-06
vg0421213186 sf0421041238 4 21213186 3.56E-07 2.43E-06
vg0910046650 sf0910045649 9 10046650 1.57E-06 1.71E-06