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 mr1887 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
vg0136326230 sf0136325187 1 36326230 1.27E-09 NA
vg0136111624 sf0136110581 1 36111624 1.23E-08 1.16E-06
vg0103442104 sf0103441104 1 3442104 1.23E-08 NA
vg0622281780 sf0622280783 6 22281780 3.41E-08 NA
vg1122526944 sf1122060815 11 22526944 3.43E-08 NA
vg0414058028 sf0414048743 4 14058028 3.77E-08 NA
vg0827372513 sf0827369799 8 27372513 9.45E-07 NA
vg0409318595 sf0409313868 4 9318595 8.35E-06 NA
vg0400154333 sf0400153333 4 154333 NA 3.27E-06
vg0622302006 sf0622301009 6 22302006 NA 3.43E-06