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 mr1771 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
vg0329922975 sf0329916014 3 29922975 5.40E-08 7.48E-07
vg0728870674 sf0728869682 7 28870674 7.44E-08 NA
vg0400672500 sf0400671499 4 672500 9.57E-08 NA
vg0706617703 sf0706616708 7 6617703 9.96E-08 NA
vg0223130772 sf0223124903 2 23130772 2.89E-06 NA
vg1111167566 sf1111161883 11 11167566 9.80E-06 NA