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 mr1580 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
vg1210372103 sf1210369516 12 10372103 1.07E-08 NA
vg1209284803 sf1209282213 12 9284803 4.64E-08 1.80E-06
vg1122446629 sf1121980500 11 22446629 6.17E-07 3.50E-06
vg1211641119 sf1211638455 12 11641119 6.71E-07 NA
vg0317479328 sf0317478110 3 17479328 1.44E-06 4.26E-06
vg1009036374 sf1008965235 10 9036374 5.18E-06 1.35E-06
vg0516302066 sf0516244548 5 16302066 7.74E-06 4.47E-06
vg0404085688 sf0404081295 4 4085688 NA 9.81E-06