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 mr1373 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
vg0505864665 sf0505864603 5 5864665 6.60E-08 6.60E-08
vg0505530975 sf0505530913 5 5530975 3.97E-07 3.97E-07
vg0224207855 sf0224201986 2 24207855 1.81E-06 1.81E-06
vg0505633780 sf0505633718 5 5633780 2.88E-06 2.88E-06
vg1222740003 sf1222706442 12 22740003 4.49E-06 4.49E-06