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 mr1235 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
vg0217033543 sf0217027673 2 17033543 2.25E-26 5.14E-22
vg0812023942 sf0812022947 8 12023942 9.65E-13 3.57E-09
vg0216721532 sf0216715662 2 16721532 1.10E-12 3.05E-09
vg0216219542 sf0216213672 2 16219542 1.91E-12 6.74E-09
vg0216663637 sf0216657767 2 16663637 1.10E-11 4.07E-08
vg0216660732 sf0216654862 2 16660732 1.40E-11 3.79E-08
vg1216424531 sf1216421824 12 16424531 3.19E-11 8.90E-07
vg0216631549 sf0216625679 2 16631549 3.94E-11 3.93E-09
vg1210467503 sf1210464916 12 10467503 5.27E-11 2.96E-07
vg0212179963 sf0212179959 2 12179963 6.61E-11 2.11E-08
vg0217737425 sf0217731555 2 17737425 3.79E-10 3.16E-07
vg0217678234 sf0217672364 2 17678234 7.12E-10 1.74E-06
vg0220342684 sf0220336816 2 20342684 3.37E-09 2.35E-06
vg0217387611 sf0217381741 2 17387611 4.71E-09 1.52E-06
vg0230571236 sf0230565367 2 30571236 1.32E-08 1.97E-06
vg0218852605 sf0218846736 2 18852605 2.21E-08 3.86E-06
vg0216773376 sf0216767506 2 16773376 3.76E-08 7.24E-07
vg0814543467 sf0814540753 8 14543467 1.83E-06 3.39E-07
vg0713784416 sf0713783423 7 13784416 NA 1.54E-07