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 mr1349 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
vg0600848094 sf0600847095 6 848094 1.27E-08 5.22E-06
vg0816447617 sf0816444903 8 16447617 5.19E-08 NA
vg0909772073 sf0909771072 9 9772073 5.16E-07 2.92E-06
vg0816379648 sf0816376934 8 16379648 1.61E-06 1.81E-06
vg0816379171 sf0816376457 8 16379171 1.82E-06 1.74E-06
vg1227262581 sf1227228981 12 27262581 NA 5.82E-07