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 mr1084 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
vg0722226606 sf0722225613 7 22226606 1.71E-08 8.42E-06
vg0316689752 sf0316688398 3 16689752 6.14E-07 3.26E-06
vg0410044585 sf0410035282 4 10044585 7.75E-07 2.45E-06
vg0324965295 sf0324963375 3 24965295 8.54E-07 3.72E-06
vg0519574921 sf0519512405 5 19574921 1.19E-06 3.10E-06
vg0613979134 sf0613978135 6 13979134 5.46E-06 2.29E-06
vg0223262220 sf0223256351 2 23262220 NA 7.62E-08