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 mr1015 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
vg0224315896 sf0224310027 2 24315896 6.16E-07 6.16E-07
vg0103511143 sf0103510143 1 3511143 9.54E-07 9.53E-07
vg0216418368 sf0216412498 2 16418368 1.73E-06 1.73E-06
vg0203460456 sf0203460454 2 3460456 1.99E-06 1.99E-06
vg0224866249 sf0224860380 2 24866249 2.86E-06 2.86E-06
vg0225825647 sf0225819778 2 25825647 3.68E-06 3.68E-06
vg0817245478 sf0817242764 8 17245478 4.06E-06 4.06E-06
vg0921364041 sf0921363560 9 21364041 4.27E-06 4.27E-06