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 mr1131 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
vg0719044633 sf0719043640 7 19044633 4.19E-35 8.88E-13
vg0304961612 sf0304960614 3 4961612 7.37E-26 NA
vg0708738726 sf0708737731 7 8738726 1.41E-25 NA
vg0715650897 sf0715649904 7 15650897 4.42E-25 NA
vg0429333406 sf0429148272 4 29333406 6.29E-25 NA
vg0719346699 sf0719345706 7 19346699 NA 8.35E-08
vg0719191462 sf0719190469 7 19191462 NA 2.73E-06
vg1207833484 sf1207830890 12 7833484 NA 3.95E-06
vg1005357442 sf1005373979 10 5357442 NA 3.97E-06