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 mr1121 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
vg0610699175 sf0610698176 6 10699175 1.38E-14 1.80E-10
vg0610545862 sf0610544863 6 10545862 4.10E-14 9.21E-11
vg0610648813 sf0610647814 6 10648813 2.60E-13 1.31E-10
vg0610364484 sf0610363485 6 10364484 2.19E-11 5.67E-08
vg0610118958 sf0610117959 6 10118958 1.50E-10 1.42E-07
vg0122819057 sf0122818013 1 22819057 8.94E-10 NA
vg0403922278 sf0403917884 4 3922278 2.31E-09 6.56E-06
vg0724465961 sf0724464967 7 24465961 3.50E-09 NA
vg1126395505 sf1125923918 11 26395505 1.38E-06 NA