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 mr1921 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
vg0205299578 sf0205299577 2 5299578 7.48E-11 4.81E-09
vg0205297301 sf0205297300 2 5297301 8.19E-11 4.40E-09
vg0726964336 sf0726963342 7 26964336 4.11E-08 NA
vg1104990849 sf1104986660 11 4990849 5.23E-08 NA
vg0726847020 sf0726846026 7 26847020 5.42E-08 3.29E-06
vg0212837159 sf0212837155 2 12837159 5.23E-07 1.38E-06
vg1124078478 sf1123612348 11 24078478 3.23E-06 3.63E-06