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 mr1325 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
vg1217549799 sf1217543754 12 17549799 1.39E-09 1.08E-08
vg1118175963 sf1117709821 11 18175963 6.90E-08 NA
vg0122692993 sf0122691948 1 22692993 6.33E-07 3.92E-07
vg1218168882 sf1218140318 12 18168882 8.16E-07 4.40E-07
vg1112803368 sf1112339689 11 12803368 NA 2.74E-06
vg0719820571 sf0719819578 7 19820571 NA 3.44E-06