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 mr1622 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
vg0407000775 sf0406996046 4 7000775 4.02E-08 2.92E-07
vg0406862676 sf0406858121 4 6862676 1.90E-07 7.71E-07
vg0809349508 sf0809348512 8 9349508 3.14E-06 8.75E-07
vg1218490229 sf1216310285 12 18490229 NA 4.15E-06
vg1007118237 sf1007133860 10 7118237 NA 4.73E-06