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 mr1637 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
vg1224470619 sf1224437073 12 24470619 4.63E-25 NA
vg0918028310 sf0918027309 9 18028310 8.36E-25 4.87E-06
vg0317321849 sf0317320659 3 17321849 6.58E-24 1.43E-06
vg0907175535 sf0907174535 9 7175535 9.47E-24 1.28E-06
vg1017935728 sf1017864500 10 17935728 1.54E-23 NA
vg0206119753 sf0206119753 2 6119753 5.49E-23 3.56E-06
vg0232755756 sf0232749887 2 32755756 1.06E-22 1.15E-06
vg0820968537 sf0820965824 8 20968537 NA 5.78E-07
vg0400678101 sf0400677100 4 678101 NA 9.15E-07
vg0211842214 sf0211842210 2 11842214 NA 1.71E-06
vg1214600105 sf1214597445 12 14600105 NA 1.76E-06