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 mr1739 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
vg0802209035 sf0802208038 8 2209035 6.86E-76 1.79E-43
vg0802032087 sf0802031090 8 2032087 1.45E-17 5.58E-07
vg0721842233 sf0721841240 7 21842233 1.86E-17 NA
vg0801959203 sf0801958206 8 1959203 3.65E-17 9.91E-08
vg0801775699 sf0801774702 8 1775699 2.96E-16 1.71E-07
vg0138428840 sf0138427797 1 38428840 4.72E-16 NA
vg0802068171 sf0802067174 8 2068171 7.18E-12 1.44E-08
vg0119708213 sf0119707168 1 19708213 1.51E-10 5.96E-07
vg0500194656 sf0500194656 5 194656 1.91E-09 NA
vg0421413370 sf0421241423 4 21413370 1.95E-09 NA
vg0802041179 sf0802040182 8 2041179 NA 4.37E-07
vg0100472638 sf0100471638 1 472638 NA 5.40E-07
vg0517761984 sf0517701625 5 17761984 NA 1.49E-06
vg0222221990 sf0222216121 2 22221990 NA 1.78E-06
vg1214525892 sf1214523233 12 14525892 NA 3.45E-06