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 mr1594 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
vg1104976483 sf1104972294 11 4976483 7.16E-09 3.90E-07
vg1104979071 sf1104974882 11 4979071 8.38E-09 3.58E-07
vg0302286724 sf0302285720 3 2286724 5.05E-08 7.96E-07
vg0334655144 sf0334648014 3 34655144 3.90E-07 1.70E-06
vg0709984451 sf0709983457 7 9984451 8.27E-07 4.23E-07
vg1015988276 sf1015917048 10 15988276 8.38E-07 2.87E-06
vg0412436211 sf0412426925 4 12436211 2.93E-06 1.68E-06
vg0223611192 sf0223605323 2 23611192 9.89E-06 2.58E-06