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 mr1011 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
vg0433925642 sf0433740539 4 33925642 1.72E-12 3.56E-08
vg0433931208 sf0433746104 4 33931208 2.65E-12 2.18E-08
vg1208070376 sf1208067782 12 8070376 2.83E-12 3.73E-06
vg1208455296 sf1208452703 12 8455296 4.15E-12 1.26E-06
vg0122505956 sf0122504911 1 22505956 1.85E-11 1.44E-06
vg0428421211 sf0428236065 4 28421211 1.38E-10 6.53E-06
vg0405618936 sf0405614377 4 5618936 4.05E-10 NA
vg0127793554 sf0127792510 1 27793554 9.94E-09 4.34E-06