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 mr1607 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
vg0140856534 sf0140855491 1 40856534 5.57E-08 NA
vg0300464166 sf0300463164 3 464166 5.69E-08 NA
vg0140575647 sf0140574604 1 40575647 5.99E-08 NA
vg0919162888 sf0919162477 9 19162888 8.63E-08 NA
vg0919172348 sf0919171938 9 19172348 1.67E-06 NA
vg1215206464 sf1215203762 12 15206464 2.43E-06 NA
vg0612730267 sf0612729268 6 12730267 5.92E-06 3.31E-06
vg0906481626 sf0906480626 9 6481626 NA 2.81E-06