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 mr1119 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
vg0421387824 sf0421215877 4 21387824 4.07E-13 4.04E-11
vg0336193973 sf0336186899 3 36193973 4.08E-12 2.57E-09
vg0504875404 sf0504875381 5 4875404 1.13E-10 1.26E-07
vg0308535729 sf0308534667 3 8535729 1.68E-10 9.59E-08
vg0915298743 sf0915297742 9 15298743 1.69E-10 2.88E-07
vg0139756098 sf0139755055 1 39756098 5.63E-10 4.85E-08
vg0727970899 sf0727969906 7 27970899 6.97E-10 1.20E-07
vg1209218924 sf1209216333 12 9218924 2.05E-09 7.99E-07
vg0625443240 sf0625442243 6 25443240 2.07E-09 8.51E-07
vg1016339056 sf1016267832 10 16339056 2.33E-09 2.80E-07
vg0142062769 sf0142061726 1 42062769 4.45E-09 9.95E-07
vg0807204233 sf0807203238 8 7204233 5.86E-09 9.03E-08
vg1201867679 sf1201866676 12 1867679 1.76E-08 1.64E-06
vg0600020896 sf0600019896 6 20896 6.15E-08 9.62E-08
vg0224173859 sf0224167990 2 24173859 8.09E-08 2.40E-07
vg0136191693 sf0136190650 1 36191693 8.63E-08 2.39E-07
vg1015855972 sf1015784742 10 15855972 8.73E-08 4.82E-07
vg1117137503 sf1116671355 11 17137503 2.09E-07 2.94E-07
vg0709963229 sf0709962235 7 9963229 NA 5.39E-07
vg0714435734 sf0714434741 7 14435734 NA 8.19E-07