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 mr1591 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
vg0822995683 sf0822992970 8 22995683 4.68E-50 5.09E-06
vg0822982462 sf0822979749 8 22982462 7.70E-50 2.36E-06
vg0206383144 sf0206383144 2 6383144 4.77E-49 2.43E-06
vg0122034730 sf0122033685 1 22034730 2.74E-48 NA
vg0922072019 sf0922071538 9 22072019 3.13E-48 NA
vg1012355269 sf1012284084 10 12355269 4.19E-48 NA
vg0523266234 sf0523203655 5 23266234 NA 5.98E-07
vg1014630581 sf1014559347 10 14630581 NA 1.54E-06
vg0310703455 sf0310702371 3 10703455 NA 2.35E-06
vg0611705308 sf0611704309 6 11705308 NA 5.97E-06