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 mr1968 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
vg0706637813 sf0706636818 7 6637813 1.51E-07 1.18E-06
vg0414202308 sf0414193024 4 14202308 1.03E-06 5.93E-08
vg0707113245 sf0707112250 7 7113245 2.66E-06 3.21E-06
vg1115246368 sf1114782682 11 15246368 5.31E-06 NA
vg0702789120 sf0702788121 7 2789120 NA 2.44E-06
vg0609448033 sf0609447034 6 9448033 NA 3.13E-06