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 mr1872 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
vg1121156657 sf1120690536 11 21156657 3.96E-07 3.97E-07
vg0133434924 sf0133433880 1 33434924 4.01E-07 4.01E-07
vg0102255943 sf0102254943 1 2255943 1.07E-06 1.07E-06
vg0820433691 sf0820430978 8 20433691 1.07E-06 1.07E-06
vg1110114810 sf1110109387 11 10114810 1.80E-06 1.80E-06
vg0138717606 sf0138716563 1 38717606 2.51E-06 2.51E-06
vg0816173019 sf0816170305 8 16173019 2.68E-06 2.68E-06
vg0407737736 sf0407733003 4 7737736 3.48E-06 3.48E-06
vg1110833634 sf1110827951 11 10833634 4.49E-06 4.49E-06