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 mr1523 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
vg0529123797 sf0529061152 5 29123797 2.69E-10 1.17E-06
vg0201493818 sf0201493818 2 1493818 6.03E-09 NA
vg0817392737 sf0817390023 8 17392737 1.61E-08 NA
vg0624096695 sf0624095698 6 24096695 2.28E-08 NA
vg0232097918 sf0232092049 2 32097918 3.12E-08 NA
vg0403119670 sf0403115273 4 3119670 1.49E-07 2.76E-06
vg0420807684 sf0420635727 4 20807684 NA 6.81E-07
vg0402256057 sf0402251652 4 2256057 NA 3.19E-06
vg0504756490 sf0504756467 5 4756490 NA 6.04E-06