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 mr1681 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
vg0919082937 sf0919082526 9 19082937 7.36E-07 7.36E-07
vg0618214950 sf0618213953 6 18214950 1.50E-06 1.50E-06
vg0508157945 sf0508157885 5 8157945 1.77E-06 1.77E-06
vg0428508285 sf0428323138 4 28508285 2.39E-06 2.39E-06
vg0919873092 sf0919872611 9 19873092 3.00E-06 3.00E-06
vg0316411183 sf0316409828 3 16411183 3.15E-06 3.15E-06
vg0316504140 sf0316502785 3 16504140 3.23E-06 3.23E-06
vg1219778717 sf1219750187 12 19778717 3.67E-06 3.67E-06