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 mr1218 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
vg1104144721 sf1104140623 11 4144721 3.64E-12 9.19E-09
vg0209430779 sf0209430777 2 9430779 6.78E-12 2.49E-08
vg0503118625 sf0503118601 5 3118625 2.05E-10 9.97E-08
vg1108842350 sf1108836960 11 8842350 3.42E-10 1.75E-06
vg0506207863 sf0506207802 5 6207863 5.51E-10 2.67E-07
vg0619482001 sf0619481004 6 19482001 1.49E-09 2.95E-06
vg0616901911 sf0616900914 6 16901911 2.33E-09 7.29E-07
vg0614119998 sf0614118999 6 14119998 3.01E-09 8.43E-07
vg0815322514 sf0815319800 8 15322514 3.76E-09 3.25E-06
vg0521689430 sf0521626872 5 21689430 6.41E-09 9.73E-07
vg1224760684 sf1224727138 12 24760684 7.05E-08 3.64E-08
vg0517105581 sf0517045222 5 17105581 3.25E-07 3.99E-06
vg0516130082 sf0516072566 5 16130082 1.13E-06 5.84E-06