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 mr1331 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
vg1002941120 sf1002940097 10 2941120 2.41E-08 2.41E-08
vg0122697050 sf0122696005 1 22697050 1.63E-07 1.63E-07
vg0406786851 sf0406782296 4 6786851 7.64E-07 7.64E-07
vg0407000775 sf0406996046 4 7000775 1.39E-06 1.39E-06
vg1216729892 sf1216723846 12 16729892 2.53E-06 2.53E-06
vg1218127441 sf1218098877 12 18127441 2.57E-06 2.57E-06
vg1218169210 sf1218140646 12 18169210 3.94E-06 3.94E-06
vg0518299665 sf0518239151 5 18299665 4.46E-06 4.46E-06
vg0921088446 sf0921087965 9 21088446 4.63E-06 4.63E-06
vg1113606688 sf1113143010 11 13606688 4.93E-06 4.94E-06
vg0131964524 sf0131963480 1 31964524 5.23E-06 5.23E-06