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 mr1822 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
vg0321576069 sf0321574579 3 21576069 1.88E-08 1.88E-08
vg1127480350 sf1127008737 11 27480350 1.43E-07 1.43E-07
vg0329703696 sf0329696736 3 29703696 1.60E-07 1.60E-07
vg0805946030 sf0805945033 8 5946030 2.97E-07 2.97E-07
vg0107079035 sf0107078035 1 7079035 2.97E-07 2.97E-07
vg0219780702 sf0219774834 2 19780702 5.58E-07 5.58E-07
vg0826077942 sf0826075228 8 26077942 8.49E-07 8.49E-07
vg1124474541 sf1124008381 11 24474541 9.34E-07 9.34E-07
vg0124420479 sf0124419435 1 24420479 1.15E-06 1.15E-06
vg1013161872 sf1013090643 10 13161872 1.27E-06 1.27E-06
vg0322174837 sf0322173344 3 22174837 1.44E-06 1.44E-06
vg0804905723 sf0804904726 8 4905723 3.84E-06 3.84E-06
vg0404762368 sf0404757807 4 4762368 4.20E-06 4.20E-06