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 mr1469 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
vg0821970212 sf0821967499 8 21970212 1.98E-09 2.32E-06
vg1214600105 sf1214597445 12 14600105 1.37E-07 3.74E-06
vg0211842214 sf0211842210 2 11842214 1.73E-06 6.51E-07
vg1212917013 sf1212914352 12 12917013 5.03E-06 NA
vg0130122521 sf0130121476 1 30122521 7.32E-06 NA