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 mr1192 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
vg0623981969 sf0623980972 6 23981969 2.88E-07 2.88E-07
vg0424956229 sf0424771090 4 24956229 1.32E-06 1.32E-06
vg0223522349 sf0223516480 2 23522349 1.45E-06 1.45E-06
vg0516885177 sf0516824818 5 16885177 1.76E-06 1.76E-06
vg0403140954 sf0403136557 4 3140954 2.71E-06 2.71E-06
vg0215856401 sf0215850531 2 15856401 2.88E-06 2.88E-06
vg0424828213 sf0424643074 4 24828213 3.40E-06 3.40E-06
vg0703290612 sf0703289613 7 3290612 4.52E-06 4.52E-06
vg0607991758 sf0607990759 6 7991758 4.87E-06 4.87E-06
vg0805826839 sf0805825842 8 5826839 4.90E-06 4.90E-06