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 mr1064 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
vg0622302006 sf0622301009 6 22302006 1.09E-11 1.01E-07
vg0626212882 sf0626211885 6 26212882 1.93E-10 1.93E-06
vg0113942268 sf0113941242 1 13942268 2.78E-10 8.22E-07
vg0626719833 sf0626718836 6 26719833 1.94E-09 1.79E-08
vg0420836689 sf0420664732 4 20836689 2.14E-09 3.62E-06
vg1200618450 sf1200617450 12 618450 3.56E-09 NA
vg0114001977 sf0114000951 1 14001977 1.04E-08 3.80E-07
vg0622510881 sf0622509884 6 22510881 1.10E-08 2.43E-06
vg0113584309 sf0113583283 1 13584309 1.19E-08 4.66E-06
vg0613373063 sf0613372064 6 13373063 1.81E-06 NA
vg0825948078 sf0825945364 8 25948078 3.37E-06 NA