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 mr1037 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
vg0620697155 sf0620696158 6 20697155 3.65E-08 7.76E-08
vg0621705457 sf0621704460 6 21705457 1.00E-07 2.33E-07
vg0817256964 sf0817254250 8 17256964 6.25E-07 5.54E-07
vg0620026942 sf0620025945 6 20026942 7.02E-07 4.97E-06
vg0920730460 sf0920729979 9 20730460 8.38E-07 1.60E-06
vg0605798825 sf0605797826 6 5798825 1.31E-06 3.45E-07
vg1002324925 sf1002323902 10 2324925 NA 4.92E-06