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 mr1231 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
vg0918923624 sf0918922624 9 18923624 3.73E-13 3.81E-09
vg0908686139 sf0908685138 9 8686139 2.43E-09 9.37E-06
vg1215476610 sf1215473907 12 15476610 2.84E-09 1.28E-07
vg0235108960 sf0235103091 2 35108960 5.48E-09 NA
vg1104399623 sf1104395525 11 4399623 8.47E-09 NA
vg0611805178 sf0611804179 6 11805178 4.39E-08 NA
vg0906170235 sf0906169235 9 6170235 1.37E-07 2.57E-07
vg0912447596 sf0912446595 9 12447596 3.47E-07 2.06E-06
vg1200937807 sf1200936807 12 937807 6.61E-07 3.87E-06
vg0615088196 sf0615087197 6 15088196 1.28E-06 8.90E-07
vg0211795124 sf0211795120 2 11795124 2.40E-06 4.02E-06