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 mr1064 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
vg0613606148 sf0613605149 6 13606148 2.06E-44 NA
vg0626679891 sf0626678894 6 26679891 3.34E-44 6.45E-06
vg0617880328 sf0617879331 6 17880328 7.97E-44 NA
vg0626712547 sf0626711550 6 26712547 9.03E-43 6.03E-07
vg0612943263 sf0612942264 6 12943263 3.43E-42 7.35E-08
vg0312494685 sf0312493403 3 12494685 1.23E-41 NA
vg0706502752 sf0706501757 7 6502752 4.03E-40 NA
vg0620767896 sf0620766899 6 20767896 7.63E-37 1.87E-08
vg0430597974 sf0430412849 4 30597974 NA 5.56E-13
vg0506631637 sf0506631578 5 6631637 NA 1.82E-07
vg0435110232 sf0434925115 4 35110232 NA 3.34E-07
vg0401635742 sf0401631291 4 1635742 NA 4.47E-07
vg0918906032 sf0918905032 9 18906032 NA 7.97E-07
vg0523302726 sf0523240147 5 23302726 NA 8.97E-07
vg0430612192 sf0430427067 4 30612192 NA 1.07E-06
vg0434883119 sf0434698010 4 34883119 NA 1.41E-06
vg0430466693 sf0430281571 4 30466693 NA 1.54E-06
vg0626730824 sf0626729827 6 26730824 NA 2.95E-06
vg1218161124 sf1218132560 12 18161124 NA 3.42E-06
vg0103031868 sf0103030868 1 3031868 NA 4.03E-06