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 mr1031 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
vg0433930554 sf0433745450 4 33930554 1.07E-11 2.11E-09
vg0526905981 sf0526843338 5 26905981 5.30E-11 8.05E-06
vg1118776907 sf1118310715 11 18776907 1.12E-10 5.98E-08
vg1208205606 sf1208203011 12 8205606 1.24E-10 NA
vg1015729829 sf1015658599 10 15729829 2.93E-10 NA
vg1208090350 sf1208087756 12 8090350 1.77E-09 2.16E-07
vg0522604659 sf0522542102 5 22604659 1.08E-08 3.97E-07
vg0224285961 sf0224280092 2 24285961 4.22E-08 1.10E-06
vg1118460774 sf1117994633 11 18460774 5.19E-08 2.03E-06
vg1019698393 sf1019626894 10 19698393 3.19E-07 NA
vg0313203063 sf0313201781 3 13203063 7.54E-07 NA
vg0527579554 sf0527516911 5 27579554 1.45E-06 NA
vg1208349628 sf1208347034 12 8349628 1.92E-06 NA
vg0804076961 sf0804075964 8 4076961 NA 6.21E-06