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 mr1606 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
vg1214656787 sf1214654127 12 14656787 8.18E-12 1.04E-07
vg1004566535 sf1004583073 10 4566535 1.43E-11 1.78E-06
vg0630464174 sf0630463176 6 30464174 9.21E-11 NA
vg0310368348 sf0310367264 3 10368348 5.63E-10 6.17E-06
vg1222231033 sf1222197580 12 22231033 8.00E-10 NA
vg1124026265 sf1123560135 11 24026265 5.01E-09 4.78E-06
vg0202453103 sf0202453101 2 2453103 6.59E-08 NA
vg0805944930 sf0805943933 8 5944930 NA 1.16E-06
vg0601563713 sf0601562714 6 1563713 NA 4.26E-06
vg0127316647 sf0127315603 1 27316647 NA 5.01E-06
vg0815304114 sf0815301400 8 15304114 NA 7.23E-06