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 mr1520 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
vg0630306971 sf0630305973 6 30306971 4.39E-10 1.27E-06
vg0306338841 sf0306337841 3 6338841 1.06E-08 NA
vg0306322887 sf0306321887 3 6322887 6.00E-08 NA
vg0922495667 sf0922495186 9 22495667 9.41E-08 3.72E-06
vg1123287295 sf1122821165 11 23287295 6.44E-07 NA
vg0413796817 sf0413787533 4 13796817 2.10E-06 1.36E-06
vg1214569048 sf1214566389 12 14569048 4.75E-06 NA