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 mr1715 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
vg0414213447 sf0414204160 4 14213447 8.71E-11 7.78E-06
vg0414170889 sf0414161605 4 14170889 2.08E-10 6.54E-07
vg0315534358 sf0315533005 3 15534358 1.46E-09 4.73E-06
vg0207140052 sf0207140052 2 7140052 1.70E-09 NA
vg0207174816 sf0207174816 2 7174816 2.63E-09 NA
vg0409314108 sf0409309381 4 9314108 3.15E-09 NA
vg1002918909 sf1002917886 10 2918909 4.05E-09 NA
vg1000261110 sf1000260110 10 261110 3.93E-08 NA
vg0314967098 sf0314965745 3 14967098 6.38E-08 NA
vg1107084198 sf1107079943 11 7084198 NA 1.90E-07