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 mr1544 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
vg0517961716 sf0517901202 5 17961716 8.29E-09 1.49E-06
vg0335289141 sf0335282010 3 35289141 5.47E-08 NA
vg0228320179 sf0228314310 2 28320179 6.69E-08 NA
vg0509233251 sf0509233180 5 9233251 3.64E-07 2.80E-06
vg0517678789 sf0517618430 5 17678789 1.12E-06 2.14E-06
vg0401473114 sf0401468664 4 1473114 2.51E-06 NA