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 mr1206 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
vg0722226606 sf0722225613 7 22226606 9.29E-10 NA
vg1011340145 sf1011268965 10 11340145 1.86E-09 NA
vg0401154727 sf0401150277 4 1154727 3.82E-09 NA
vg0428761895 sf0428576746 4 28761895 1.07E-08 NA
vg0402377656 sf0402373251 4 2377656 1.11E-08 NA
vg1125126374 sf1124660214 11 25126374 2.03E-08 NA
vg0613121902 sf0613120903 6 13121902 2.10E-07 2.09E-06
vg0616884771 sf0616883774 6 16884771 6.33E-07 NA
vg0613979134 sf0613978135 6 13979134 1.03E-06 2.19E-06