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 mr1994 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
vg1121561182 sf1121095059 11 21561182 7.34E-10 1.93E-08
vg1121561284 sf1121095161 11 21561284 2.62E-09 8.44E-08
vg1128863899 sf1128340678 11 28863899 2.89E-08 9.42E-07
vg0227089280 sf0227083411 2 27089280 8.96E-07 4.07E-06
vg1000990951 sf1000989927 10 990951 5.03E-06 2.66E-06