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 mr1214 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
vg0910734707 sf0910733706 9 10734707 6.84E-07 6.84E-07
vg1215352870 sf1215350168 12 15352870 1.28E-06 1.28E-06
vg0433246740 sf0433061628 4 33246740 2.07E-06 2.07E-06
vg0106330325 sf0106329325 1 6330325 2.11E-06 2.11E-06
vg0433298009 sf0433112897 4 33298009 2.46E-06 2.46E-06
vg0323664940 sf0323663114 3 23664940 2.79E-06 2.79E-06
vg1117664827 sf1117198683 11 17664827 3.25E-06 3.25E-06
vg1022847222 sf1022775695 10 22847222 4.38E-06 4.38E-06