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 mr1596 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
vg1219413533 sf1219385003 12 19413533 1.02E-08 NA
vg1125009665 sf1124543505 11 25009665 1.54E-08 NA
vg0314645812 sf0314644499 3 14645812 2.05E-08 NA
vg0128501511 sf0128500466 1 28501511 3.57E-08 NA
vg0425061026 sf0424875887 4 25061026 3.69E-08 9.04E-06
vg0702624412 sf0702623413 7 2624412 7.02E-08 6.43E-06
vg1125700572 sf1125234411 11 25700572 7.48E-08 NA
vg0314873937 sf0314872584 3 14873937 9.77E-06 NA