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 mr1402 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
vg0406526555 sf0406521998 4 6526555 3.50E-43 1.24E-06
vg0406561841 sf0406557284 4 6561841 8.59E-43 1.76E-06
vg0913374139 sf0913373138 9 13374139 5.75E-41 6.83E-06
vg0617179682 sf0617178685 6 17179682 8.62E-41 NA
vg0614431150 sf0614430151 6 14431150 3.00E-40 NA
vg0804052403 sf0804051406 8 4052403 1.76E-38 NA
vg0613063818 sf0613062819 6 13063818 2.73E-37 1.29E-06
vg0911437019 sf0911436018 9 11437019 NA 7.99E-06