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 mr1421 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
vg1104978992 sf1104974803 11 4978992 4.79E-09 2.59E-06
vg0130736864 sf0130735820 1 30736864 5.03E-09 6.81E-06
vg1104990849 sf1104986660 11 4990849 5.14E-09 2.04E-06
vg0726964336 sf0726963342 7 26964336 5.94E-08 NA
vg0805546679 sf0805545682 8 5546679 9.52E-08 NA
vg0300249514 sf0300248514 3 249514 2.26E-07 4.05E-07
vg0820969276 sf0820966563 8 20969276 1.74E-06 NA
vg1106375766 sf1106371518 11 6375766 7.36E-06 3.41E-06