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 mr1524 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
vg0330512638 sf0330505527 3 30512638 2.61E-09 2.61E-09
vg1104743483 sf1104739385 11 4743483 2.38E-07 2.38E-07
vg0122336837 sf0122335792 1 22336837 4.80E-07 4.80E-07
vg0309399006 sf0309397942 3 9399006 1.19E-06 1.19E-06
vg0321595057 sf0321593567 3 21595057 1.44E-06 1.44E-06
vg0432816657 sf0432631543 4 32816657 3.79E-06 3.79E-06