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 mr1562 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
vg0706162756 sf0706161757 7 6162756 5.54E-09 1.31E-06
vg0605513869 sf0605512870 6 5513869 1.54E-08 1.92E-06
vg0525016334 sf0524953749 5 25016334 3.16E-08 NA
vg1204111654 sf1204110642 12 4111654 5.20E-08 8.39E-06
vg0431515534 sf0431330433 4 31515534 5.90E-08 4.54E-06
vg1208634025 sf1208631432 12 8634025 1.07E-07 3.72E-06
vg0821970212 sf0821967499 8 21970212 NA 3.20E-06