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 mr1938 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
vg0525590896 sf0525528317 5 25590896 7.59E-09 5.16E-07
vg0526218893 sf0526156257 5 26218893 1.94E-08 3.64E-07
vg0217654440 sf0217648570 2 17654440 5.72E-08 2.26E-06
vg0311297778 sf0311296496 3 11297778 2.19E-07 3.12E-06
vg1116933718 sf1116468597 11 16933718 NA 3.53E-06