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 mr1913 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
vg0406420728 sf0406416168 4 6420728 2.63E-46 3.87E-21
vg0406422637 sf0406418077 4 6422637 5.88E-44 1.47E-23
vg0406631705 sf0406627149 4 6631705 9.86E-39 5.26E-11
vg0305540812 sf0305539812 3 5540812 7.19E-38 NA
vg1020860458 sf1020788937 10 20860458 1.78E-37 NA
vg1002581783 sf1002580760 10 2581783 5.20E-37 NA
vg0800421304 sf0800420304 8 421304 8.11E-37 NA
vg0725403826 sf0725402832 7 25403826 6.82E-32 9.61E-07
vg0122848570 sf0122847526 1 22848570 2.07E-31 6.90E-07
vg0222746794 sf0222740925 2 22746794 NA 4.34E-19
vg0222747179 sf0222741310 2 22747179 NA 8.47E-19
vg0406521772 sf0406517215 4 6521772 NA 1.88E-11
vg0406532594 sf0406528037 4 6532594 NA 9.77E-11
vg0406361314 sf0406356754 4 6361314 NA 5.10E-10
vg0222725003 sf0222719134 2 22725003 NA 1.98E-09
vg0223753517 sf0223747648 2 23753517 NA 2.07E-09
vg0406513963 sf0406509406 4 6513963 NA 3.46E-09
vg0222817468 sf0222811599 2 22817468 NA 1.24E-08
vg0406537255 sf0406532698 4 6537255 NA 2.98E-08
vg0222833462 sf0222827593 2 22833462 NA 3.96E-07
vg1001281495 sf1001280472 10 1281495 NA 8.21E-07
vg0233608236 sf0233602367 2 33608236 NA 1.17E-06
vg1007790601 sf1007806211 10 7790601 NA 2.81E-06
vg0912877788 sf0912876787 9 12877788 NA 2.90E-06
vg0406489664 sf0406485107 4 6489664 NA 2.95E-06
vg0817329442 sf0817326728 8 17329442 NA 3.86E-06
vg1016498197 sf1016426970 10 16498197 NA 4.26E-06
vg1223902919 sf1223869372 12 23902919 NA 4.79E-06