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 mr1978 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
vg0222019290 sf0222013421 2 22019290 2.31E-09 2.31E-09
vg0702566842 sf0702565843 7 2566842 5.35E-08 5.35E-08
vg1224906898 sf1224873352 12 24906898 1.64E-07 1.64E-07
vg0321905521 sf0321904030 3 21905521 2.00E-07 2.00E-07
vg0142965130 sf0142964086 1 42965130 1.87E-06 1.87E-06
vg0314262681 sf0314261370 3 14262681 1.95E-06 1.95E-06
vg0324547776 sf0324545855 3 24547776 2.08E-06 2.08E-06
vg0614455569 sf0614454570 6 14455569 2.44E-06 2.44E-06
vg0910045544 sf0910044543 9 10045544 3.76E-06 3.77E-06
vg0321154919 sf0321153429 3 21154919 4.85E-06 4.85E-06
vg0335773756 sf0335766625 3 35773756 8.42E-06 8.42E-06