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 mr1867 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
vg1120968854 sf1120502731 11 20968854 1.05E-06 1.05E-06
vg0511016076 sf0511016005 5 11016076 1.15E-06 1.15E-06
vg0321991531 sf0321990038 3 21991531 1.38E-06 1.38E-06
vg0907516066 sf0907515066 9 7516066 1.79E-06 1.78E-06
vg0415693361 sf0415654672 4 15693361 2.26E-06 2.26E-06
vg0509093004 sf0509092932 5 9093004 2.81E-06 2.81E-06
vg0329073998 sf0329067050 3 29073998 3.07E-06 3.07E-06
vg0109949717 sf0109948693 1 9949717 3.50E-06 3.51E-06
vg1020967265 sf1020895744 10 20967265 4.81E-06 4.82E-06