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 mr1874 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
vg0825037085 sf0825034371 8 25037085 1.36E-35 6.74E-29
vg0825510141 sf0825507427 8 25510141 1.63E-15 1.30E-10
vg0825178332 sf0825175618 8 25178332 1.58E-12 3.54E-08
vg0825175613 sf0825172899 8 25175613 3.72E-12 1.69E-10
vg0825074071 sf0825071357 8 25074071 1.27E-11 1.58E-06
vg0825099238 sf0825096524 8 25099238 2.61E-11 3.10E-12
vg1104513762 sf1104509664 11 4513762 5.68E-11 2.38E-08
vg0825151239 sf0825148525 8 25151239 6.77E-11 1.79E-08
vg0825103406 sf0825100692 8 25103406 1.40E-09 1.68E-08
vg1015565858 sf1015494628 10 15565858 1.56E-07 1.88E-06
vg1009610847 sf1009539668 10 9610847 4.80E-07 2.70E-07
vg1216037604 sf1216034900 12 16037604 8.59E-06 2.01E-06
vg0825239616 sf0825236902 8 25239616 NA 1.36E-06