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 mr1482 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
vg0507296732 sf0507296674 5 7296732 6.35E-09 NA
vg0821970212 sf0821967499 8 21970212 9.91E-09 1.10E-06
vg0526321786 sf0526259149 5 26321786 1.00E-08 NA
vg0217654440 sf0217648570 2 17654440 1.69E-08 NA
vg0220551014 sf0220545146 2 20551014 2.09E-08 NA
vg1202542327 sf1202541329 12 2542327 4.07E-06 NA
vg0919860219 sf0919859738 9 19860219 4.22E-06 NA
vg0428041203 sf0427856067 4 28041203 6.39E-06 NA
vg0231688782 sf0231682913 2 31688782 NA 1.84E-06