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 mr1438 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
vg1105687383 sf1105683135 11 5687383 3.36E-08 7.63E-06
vg0142322025 sf0142320981 1 42322025 4.21E-08 NA
vg0303196783 sf0303195779 3 3196783 6.16E-06 NA
vg0626772403 sf0626771406 6 26772403 8.86E-06 1.28E-06
vg0914741739 sf0914740738 9 14741739 NA 2.36E-06