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 mr1522 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
vg1104295774 sf1104291676 11 4295774 1.68E-08 1.95E-06
vg1104295772 sf1104291674 11 4295772 1.88E-08 1.13E-06
vg1218169641 sf1218141077 12 18169641 8.07E-07 1.22E-06
vg0219427804 sf0219421936 2 19427804 1.06E-06 NA
vg0336051407 sf0336044276 3 36051407 1.06E-06 NA
vg1125478932 sf1125012771 11 25478932 2.15E-06 4.01E-06
vg1126223877 sf1125752291 11 26223877 NA 3.43E-06
vg0614865428 sf0614864429 6 14865428 NA 4.77E-06