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 mr1262 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
vg1214625010 sf1214622350 12 14625010 1.74E-08 2.30E-06
vg1214656787 sf1214654127 12 14656787 2.68E-08 1.26E-06
vg1214810366 sf1214807707 12 14810366 3.83E-08 1.63E-06
vg0719513815 sf0719512822 7 19513815 5.01E-08 9.76E-06
vg0421498214 sf0421326265 4 21498214 6.65E-07 6.76E-07
vg0914989711 sf0914988710 9 14989711 NA 6.28E-06