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 mr1246 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
vg0719011406 sf0719010413 7 19011406 1.69E-98 5.37E-26
vg0917780861 sf0917779860 9 17780861 4.82E-74 NA
vg0918588322 sf0918587321 9 18588322 5.58E-73 3.51E-07
vg0705232840 sf0705231841 7 5232840 3.31E-72 NA
vg0220874371 sf0220868503 2 20874371 5.40E-71 NA
vg0725752399 sf0725751405 7 25752399 6.57E-71 NA
vg0215798562 sf0215792692 2 15798562 2.03E-63 1.25E-06
vg0719091461 sf0719090468 7 19091461 NA 4.69E-22
vg0718955684 sf0718954691 7 18955684 NA 6.25E-13
vg0719071513 sf0719070520 7 19071513 NA 6.04E-12
vg0719045166 sf0719044173 7 19045166 NA 9.95E-12
vg0719087266 sf0719086273 7 19087266 NA 8.45E-11
vg0719140918 sf0719139925 7 19140918 NA 4.26E-10
vg0718886202 sf0718885209 7 18886202 NA 5.86E-10
vg0719346699 sf0719345706 7 19346699 NA 4.21E-09
vg0719466615 sf0719465622 7 19466615 NA 1.34E-07
vg0718996077 sf0718995084 7 18996077 NA 3.79E-07
vg0719432601 sf0719431608 7 19432601 NA 9.95E-07
vg0228211032 sf0228205163 2 28211032 NA 1.31E-06
vg1010998659 sf1010927479 10 10998659 NA 1.67E-06
vg0228211068 sf0228205199 2 28211068 NA 3.37E-06