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 mr1969 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
vg0405710877 sf0405706316 4 5710877 1.46E-15 NA
vg0101546196 sf0101545196 1 1546196 5.24E-15 NA
vg0919811177 sf0919810696 9 19811177 5.17E-14 NA
vg0402158888 sf0402154483 4 2158888 6.90E-13 NA
vg0412723669 sf0412714380 4 12723669 7.13E-13 NA
vg0431442016 sf0431256914 4 31442016 3.68E-11 NA
vg1118334692 sf1117868550 11 18334692 4.41E-11 8.76E-06
vg1123700733 sf1123234603 11 23700733 1.19E-10 NA