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 mr1584 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
vg0728265516 sf0728264524 7 28265516 7.89E-15 4.21E-07
vg1213797816 sf1213795154 12 13797816 5.44E-14 NA
vg0313144137 sf0313142855 3 13144137 1.73E-12 NA
vg1022746980 sf1022675454 10 22746980 4.08E-12 NA
vg1217106453 sf1217100408 12 17106453 5.50E-12 NA
vg1221512382 sf1221478929 12 21512382 3.74E-10 NA
vg1102677343 sf1102673247 11 2677343 7.95E-10 3.86E-06
vg0413769010 sf0413759724 4 13769010 NA 3.04E-06
vg0413762842 sf0413753556 4 13762842 NA 3.09E-06