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 mr1157 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
vg0202909303 sf0202909301 2 2909303 9.75E-12 NA
vg1116564255 sf1116099133 11 16564255 1.26E-11 NA
vg0625109737 sf0625108740 6 25109737 1.82E-11 NA
vg0916882610 sf0916881609 9 16882610 3.80E-11 NA
vg0602870012 sf0602869013 6 2870012 9.17E-11 NA
vg0522983676 sf0522921117 5 22983676 1.61E-09 NA
vg1012313676 sf1012242491 10 12313676 2.11E-09 NA
vg1107373570 sf1107369315 11 7373570 1.12E-06 NA
vg0820146322 sf0820143609 8 20146322 NA 1.39E-06
vg0103143509 sf0103142509 1 3143509 NA 3.71E-06