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 mr1876 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
vg0906503065 sf0906502065 9 6503065 1.98E-09 1.76E-06
vg0223518528 sf0223512659 2 23518528 3.28E-08 NA
vg0125460828 sf0125459784 1 25460828 4.15E-08 NA
vg0304597758 sf0304596760 3 4597758 5.21E-08 NA
vg1210371272 sf1210368685 12 10371272 3.73E-06 4.69E-07
vg1214656787 sf1214654127 12 14656787 NA 2.84E-06
vg1219662811 sf1219634281 12 19662811 NA 4.03E-06
vg1214609973 sf1214607313 12 14609973 NA 4.68E-06
vg0317132280 sf0317131094 3 17132280 NA 4.89E-06
vg1018654736 sf1018583294 10 18654736 NA 5.71E-06