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 mr1551 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
vg0506124564 sf0506124503 5 6124564 3.05E-08 1.93E-07
vg0229918162 sf0229912293 2 29918162 6.51E-08 2.66E-06
vg0712894798 sf0712893805 7 12894798 3.62E-07 1.81E-06
vg0629505680 sf0629504682 6 29505680 1.63E-06 2.85E-06
vg1107275983 sf1107271728 11 7275983 3.52E-06 NA
vg0709981442 sf0709980448 7 9981442 4.11E-06 NA