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 mr1208 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
vg0114278961 sf0114277935 1 14278961 3.60E-08 2.37E-07
vg0922061048 sf0922060567 9 22061048 9.99E-08 1.35E-06
vg0909958821 sf0909957820 9 9958821 1.93E-07 7.25E-07
vg0114135723 sf0114134697 1 14135723 1.96E-07 3.97E-06
vg0729266134 sf0729265142 7 29266134 7.65E-07 NA