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 mr1575 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
vg0518984986 sf0518922470 5 18984986 1.90E-18 5.48E-07
vg1215403123 sf1215400421 12 15403123 3.54E-18 2.71E-06
vg0805968808 sf0805967811 8 5968808 5.50E-18 4.77E-06
vg1219748904 sf1219720374 12 19748904 6.52E-18 4.87E-06
vg0820967741 sf0820965028 8 20967741 7.58E-18 7.45E-07
vg1215090096 sf1215087437 12 15090096 1.21E-17 1.40E-06
vg1004566535 sf1004583073 10 4566535 1.88E-16 2.67E-06
vg1221719215 sf1221685762 12 21719215 3.40E-14 3.83E-06