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 mr1719 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
vg0305409075 sf0305408075 3 5409075 1.82E-45 1.68E-07
vg0407118586 sf0407113856 4 7118586 3.61E-42 1.64E-06
vg1219203688 sf1219175158 12 19203688 4.07E-42 1.60E-07
vg0409861333 sf0409852031 4 9861333 4.70E-42 NA
vg0617365911 sf0617364914 6 17365911 9.97E-42 2.03E-06
vg0324379515 sf0324377594 3 24379515 1.88E-40 2.30E-08
vg0409446663 sf0409437361 4 9446663 7.71E-40 1.15E-06
vg0820512018 sf0820509305 8 20512018 5.40E-37 4.55E-06
vg0918823110 sf0918822110 9 18823110 NA 1.62E-07
vg0235925623 sf0235919754 2 35925623 NA 2.45E-07
vg0614114702 sf0614113703 6 14114702 NA 1.14E-06
vg0714224732 sf0714223739 7 14224732 NA 1.22E-06
vg0721382199 sf0721381206 7 21382199 NA 1.43E-06
vg1201039384 sf1201038384 12 1039384 NA 1.61E-06
vg0421348658 sf0421176712 4 21348658 NA 1.87E-06
vg1213065651 sf1213062990 12 13065651 NA 2.30E-06
vg0411580106 sf0411570810 4 11580106 NA 2.62E-06
vg0908838284 sf0908837283 9 8838284 NA 3.10E-06
vg0412903510 sf0412894218 4 12903510 NA 3.55E-06
vg1201876125 sf1201875122 12 1876125 NA 3.76E-06
vg0715846947 sf0715845954 7 15846947 NA 4.77E-06