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 mr1442 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
vg1214656841 sf1214654181 12 14656841 4.67E-07 NA
vg0231289965 sf0231284096 2 31289965 9.69E-07 4.84E-06
vg0709674724 sf0709673730 7 9674724 1.75E-06 NA
vg1108255008 sf1108249618 11 8255008 3.67E-06 1.13E-07
vg0617549004 sf0617548007 6 17549004 5.90E-06 NA
vg0907175556 sf0907174556 9 7175556 NA 2.32E-06
vg0224434814 sf0224428945 2 24434814 NA 4.26E-06