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 mr1617 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
vg0604281708 sf0604280709 6 4281708 6.42E-18 2.80E-11
vg0604336777 sf0604335778 6 4336777 2.36E-17 1.78E-11
vg0727913447 sf0727912454 7 27913447 1.79E-11 NA
vg0508706913 sf0508706841 5 8706913 3.58E-11 NA
vg0609215665 sf0609214666 6 9215665 1.10E-10 NA
vg0514667369 sf0514609912 5 14667369 1.20E-10 NA
vg0604356746 sf0604355747 6 4356746 1.90E-07 6.77E-07
vg0601454762 sf0601453763 6 1454762 1.71E-06 3.46E-06