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 mr1387 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
vg0224869035 sf0224863166 2 24869035 1.66E-08 1.52E-06
vg0426278854 sf0426093727 4 26278854 4.86E-08 NA
vg1222302853 sf1222269400 12 22302853 8.48E-08 1.33E-06
vg0708445190 sf0708444195 7 8445190 9.65E-08 4.53E-06
vg0411006495 sf0410997196 4 11006495 1.88E-07 1.82E-06
vg0301209725 sf0301208723 3 1209725 1.89E-06 3.71E-06
vg0706102792 sf0706101793 7 6102792 2.20E-06 8.54E-06