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 mr1787 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
vg0720257973 sf0720256980 7 20257973 2.04E-08 NA
vg0405832157 sf0405827596 4 5832157 2.55E-08 NA
vg0422579943 sf0422394826 4 22579943 2.70E-08 NA
vg1216161719 sf1216159015 12 16161719 2.73E-08 NA
vg1113073660 sf1112609981 11 13073660 2.79E-08 9.78E-06
vg0124060257 sf0124059213 1 24060257 5.32E-08 4.37E-06
vg0405832147 sf0405827586 4 5832147 1.02E-07 NA