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 mr1459 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
vg1127982448 sf1127510834 11 27982448 1.25E-07 1.25E-07
vg0323589698 sf0323587872 3 23589698 2.83E-07 2.83E-07
vg0332498725 sf0332491598 3 32498725 1.56E-06 1.56E-06
vg0922565216 sf0922564735 9 22565216 1.72E-06 1.72E-06
vg0129974508 sf0129973463 1 29974508 2.15E-06 2.15E-06
vg0328101436 sf0328094490 3 28101436 2.81E-06 2.80E-06
vg1224035880 sf1224002333 12 24035880 3.12E-06 3.12E-06
vg0624640412 sf0624639415 6 24640412 3.35E-06 3.36E-06
vg0529106995 sf0529044350 5 29106995 3.64E-06 3.65E-06
vg0230504954 sf0230499085 2 30504954 4.18E-06 4.18E-06
vg1008380500 sf1008309362 10 8380500 4.61E-06 4.62E-06