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 mr1128 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
vg0130670983 sf0130669939 1 30670983 5.31E-12 5.31E-12
vg0135794714 sf0135793671 1 35794714 4.10E-07 4.10E-07
vg0707270813 sf0707269818 7 7270813 5.84E-07 5.84E-07
vg1203606223 sf1203605222 12 3606223 1.19E-06 1.19E-06
vg0134084052 sf0134083008 1 34084052 1.39E-06 1.39E-06
vg0123987202 sf0123986158 1 23987202 1.81E-06 1.81E-06
vg1225934717 sf1225901111 12 25934717 1.95E-06 1.95E-06
vg0704803343 sf0704802344 7 4803343 3.18E-06 3.18E-06
vg0805134129 sf0805133132 8 5134129 3.29E-06 3.29E-06
vg0123496865 sf0123495821 1 23496865 3.54E-06 3.54E-06