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 mr1353 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
vg1215174174 sf1215171510 12 15174174 8.05E-07 8.05E-07
vg1122446629 sf1121980500 11 22446629 1.04E-06 1.04E-06
vg1017098057 sf1017026829 10 17098057 1.09E-06 1.09E-06
vg0406854976 sf0406850421 4 6854976 1.34E-06 1.34E-06
vg0114249827 sf0114248801 1 14249827 1.73E-06 1.73E-06
vg1001246161 sf1001245138 10 1246161 2.49E-06 2.49E-06
vg0140479964 sf0140478921 1 40479964 4.10E-06 4.10E-06