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 mr1085 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
vg0719307663 sf0719306670 7 19307663 1.14E-13 1.14E-13
vg0719413496 sf0719412503 7 19413496 4.35E-13 4.34E-13
vg0719006525 sf0719005532 7 19006525 2.07E-12 2.06E-12
vg0107198487 sf0107197487 1 7198487 5.21E-08 5.21E-08
vg1100694812 sf1100693815 11 694812 5.56E-08 5.56E-08
vg1215998905 sf1215996201 12 15998905 8.19E-08 8.19E-08
vg0828152822 sf0828150108 8 28152822 1.07E-07 1.07E-07
vg0900544466 sf0900543466 9 544466 1.48E-07 1.48E-07
vg0321781118 sf0321779628 3 21781118 2.98E-07 2.98E-07
vg0417365619 sf0417193662 4 17365619 4.30E-07 4.30E-07
vg0228933475 sf0228927606 2 28933475 4.49E-07 4.48E-07
vg0326113283 sf0326111302 3 26113283 5.26E-07 5.26E-07
vg0328527072 sf0328520125 3 28527072 6.05E-07 6.05E-07
vg0406192421 sf0406187861 4 6192421 7.35E-07 7.35E-07
vg0903048899 sf0903047899 9 3048899 7.82E-07 7.82E-07
vg0227635783 sf0227629914 2 27635783 9.48E-07 9.48E-07
vg0109816587 sf0109815563 1 9816587 9.91E-07 9.90E-07
vg0405706633 sf0405702072 4 5706633 1.17E-06 1.17E-06
vg1226051767 sf1226018161 12 26051767 1.25E-06 1.25E-06
vg0700559381 sf0700558381 7 559381 1.30E-06 1.30E-06
vg0132393866 sf0132392822 1 32393866 1.42E-06 1.42E-06