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 mr1537 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
vg1104978992 sf1104974803 11 4978992 2.62E-08 2.62E-08
vg1104947437 sf1104943248 11 4947437 1.19E-06 1.19E-06
vg0523209688 sf0523147129 5 23209688 1.45E-06 1.45E-06
vg1105750981 sf1105746733 11 5750981 1.74E-06 1.74E-06
vg0119599113 sf0119598068 1 19599113 2.63E-06 2.63E-06
vg0904153122 sf0904152122 9 4153122 3.92E-06 3.92E-06
vg0219352023 sf0219346155 2 19352023 4.24E-06 4.24E-06