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 mr1428 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
vg0119676181 sf0119675136 1 19676181 1.51E-11 NA
vg0123716192 sf0123715148 1 23716192 1.64E-11 NA
vg0132722397 sf0132721353 1 32722397 4.66E-11 NA
vg0621539752 sf0621538755 6 21539752 2.40E-10 NA
vg0612996928 sf0612995929 6 12996928 2.49E-10 NA
vg1103155824 sf1103151727 11 3155824 2.79E-06 NA
vg0918902466 sf0918901466 9 18902466 2.98E-06 NA
vg0614982179 sf0614981180 6 14982179 5.12E-06 NA
vg0123560913 sf0123559869 1 23560913 5.48E-06 3.86E-06
vg1124647675 sf1124181515 11 24647675 NA 3.27E-06
vg1223833401 sf1223799854 12 23833401 NA 8.66E-06