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 mr1966 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
vg1120840098 sf1120374001 11 20840098 1.04E-06 1.04E-06
vg0119798012 sf0119796967 1 19798012 1.06E-06 1.06E-06
vg0622374528 sf0622373531 6 22374528 1.94E-06 1.94E-06
vg1216483033 sf1216480326 12 16483033 2.03E-06 2.03E-06
vg0407001583 sf0406996854 4 7001583 2.37E-06 2.36E-06
vg0406812732 sf0406808177 4 6812732 2.47E-06 2.46E-06
vg1014702877 sf1014631643 10 14702877 4.65E-06 4.64E-06
vg0129458284 sf0129457239 1 29458284 9.17E-06 9.16E-06