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 mr1820 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
vg0821970212 sf0821967499 8 21970212 8.45E-08 4.84E-06
vg1214600105 sf1214597445 12 14600105 9.26E-07 8.46E-06
vg0131535738 sf0131534694 1 31535738 1.40E-06 NA
vg1210371272 sf1210368685 12 10371272 2.22E-06 4.71E-06
vg0518984986 sf0518922470 5 18984986 NA 8.74E-07