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 mr1441 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
vg0222725881 sf0222720012 2 22725881 1.24E-39 2.24E-21
vg0222742146 sf0222736277 2 22742146 2.57E-39 1.62E-21
vg0223176714 sf0223170845 2 23176714 9.87E-16 1.23E-07
vg0222624829 sf0222618960 2 22624829 1.72E-11 1.60E-06
vg0224676560 sf0224670691 2 24676560 1.29E-10 NA
vg1112606104 sf1112142307 11 12606104 5.45E-10 NA
vg1203611892 sf1203610891 12 3611892 1.57E-09 3.27E-07
vg0222656032 sf0222650163 2 22656032 1.75E-09 1.26E-09
vg0223737012 sf0223731143 2 23737012 2.11E-09 3.47E-06
vg0313678497 sf0313677214 3 13678497 2.74E-08 NA
vg0209427613 sf0209427611 2 9427613 7.07E-08 5.47E-06
vg1216729892 sf1216723846 12 16729892 NA 5.35E-06