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 mr1743 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
vg1216058319 sf1216055615 12 16058319 9.48E-10 2.20E-06
vg1216059901 sf1216057197 12 16059901 1.40E-09 1.09E-06
vg1217497177 sf1217491132 12 17497177 5.29E-08 NA
vg0600686096 sf0600685097 6 686096 6.67E-08 NA
vg0706528880 sf0706527885 7 6528880 5.18E-07 1.36E-06
vg1125603056 sf1125136895 11 25603056 3.87E-06 NA
vg1221429605 sf1221396152 12 21429605 5.00E-06 NA
vg0626806805 sf0626805808 6 26806805 NA 2.62E-06
vg0626798346 sf0626797349 6 26798346 NA 2.81E-06
vg0723280519 sf0723279526 7 23280519 NA 4.07E-06