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 mr1470 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
vg1218074718 sf1218046154 12 18074718 9.51E-08 1.71E-06
vg0914837473 sf0914836472 9 14837473 3.10E-07 4.10E-07
vg0111837647 sf0111836621 1 11837647 3.70E-07 1.74E-06
vg1121947567 sf1121481438 11 21947567 1.68E-06 4.22E-06
vg0328927205 sf0328920257 3 28927205 2.05E-06 1.64E-06