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 mr1380 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
vg0112495464 sf0112494438 1 12495464 4.68E-08 NA
vg1121385012 sf1120918889 11 21385012 6.71E-08 7.26E-06
vg0901631141 sf0901630141 9 1631141 1.74E-07 4.36E-06
vg0227036650 sf0227030781 2 27036650 2.48E-07 NA
vg1016281680 sf1016210456 10 16281680 3.37E-06 NA