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 mr1934 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
vg0524585970 sf0524523390 5 24585970 4.63E-44 2.05E-25
vg1100512559 sf1100511562 11 512559 2.10E-19 5.46E-06
vg0524354930 sf0524292351 5 24354930 1.35E-14 NA
vg1200003632 sf1200002632 12 3632 2.24E-14 NA
vg1122487776 sf1122021647 11 22487776 7.73E-14 4.96E-07
vg1205231921 sf1205230907 12 5231921 1.04E-13 1.55E-06
vg1122446629 sf1121980500 11 22446629 4.63E-13 NA
vg1122459168 sf1121993039 11 22459168 8.11E-13 9.56E-08
vg0524400543 sf0524337964 5 24400543 2.41E-12 6.13E-07
vg0526374495 sf0526311858 5 26374495 NA 4.77E-07
vg0714958893 sf0714957900 7 14958893 NA 1.94E-06
vg0921359292 sf0921358811 9 21359292 NA 3.43E-06
vg0215098859 sf0215092989 2 15098859 NA 3.88E-06