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 mr1987 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
vg0317756145 sf0317754927 3 17756145 1.26E-14 5.04E-10
vg0322565972 sf0322564461 3 22565972 1.91E-14 5.78E-11
vg0319079018 sf0319077778 3 19079018 2.38E-10 6.96E-07
vg0319775799 sf0319774310 3 19775799 2.64E-10 4.14E-06
vg0322901276 sf0322899765 3 22901276 4.48E-10 2.60E-07
vg0320508322 sf0320506833 3 20508322 5.68E-10 3.38E-06
vg0321218638 sf0321217148 3 21218638 1.28E-09 4.95E-07
vg0323945949 sf0323944123 3 23945949 1.46E-09 1.91E-07
vg0324083783 sf0324081862 3 24083783 6.71E-09 5.05E-07
vg1216729091 sf1216723045 12 16729091 7.81E-09 3.35E-06
vg0318193307 sf0318192089 3 18193307 9.98E-09 2.58E-06
vg0321772541 sf0321771051 3 21772541 1.26E-08 1.22E-06
vg0320662648 sf0320661158 3 20662648 3.55E-08 4.73E-06
vg0318866067 sf0318864827 3 18866067 6.52E-08 1.29E-06
vg0808279687 sf0808278691 8 8279687 1.01E-07 1.37E-06
vg1106375766 sf1106371518 11 6375766 NA 2.91E-06
vg1219351662 sf1219323132 12 19351662 NA 9.18E-06