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 mr1852 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
vg0819484748 sf0819482035 8 19484748 5.30E-13 3.71E-08
vg0317860149 sf0317858931 3 17860149 2.97E-11 2.84E-06
vg0320452783 sf0320451294 3 20452783 2.56E-10 NA
vg0823915309 sf0823912595 8 23915309 3.40E-10 NA
vg0315182111 sf0315180758 3 15182111 3.81E-10 NA
vg0818778107 sf0818775394 8 18778107 4.01E-10 1.56E-06
vg1124477987 sf1124011827 11 24477987 5.83E-10 1.28E-07
vg0911503277 sf0911502276 9 11503277 NA 4.06E-06