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 mr1087 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
vg0610455473 sf0610454474 6 10455473 8.04E-21 3.18E-12
vg0610723942 sf0610722943 6 10723942 1.52E-20 8.71E-13
vg0613393025 sf0613392026 6 13393025 1.20E-14 NA
vg0617149052 sf0617148055 6 17149052 1.23E-14 NA
vg1225125551 sf1225092005 12 25125551 3.54E-14 NA
vg0516387684 sf0516330166 5 16387684 6.36E-14 NA
vg0610648813 sf0610647814 6 10648813 6.30E-12 2.78E-09
vg0610752378 sf0610751379 6 10752378 5.01E-11 1.06E-09
vg0610059822 sf0610058823 6 10059822 5.53E-10 3.86E-08
vg0610489279 sf0610488280 6 10489279 1.84E-09 1.16E-06
vg1201642245 sf1201641245 12 1642245 NA 1.77E-06
vg0222276877 sf0222271008 2 22276877 NA 2.43E-06
vg0610693135 sf0610692136 6 10693135 NA 3.16E-06