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 mr1961 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
vg0141320383 sf0141319340 1 41320383 1.27E-10 1.57E-08
vg0108582948 sf0108581948 1 8582948 5.84E-10 7.31E-08
vg0807204233 sf0807203238 8 7204233 3.04E-09 3.65E-06
vg0918787679 sf0918786679 9 18787679 4.58E-09 NA
vg0915284648 sf0915283647 9 15284648 4.67E-09 NA
vg0600020896 sf0600019896 6 20896 1.72E-08 1.14E-06
vg0424049928 sf0423864789 4 24049928 2.07E-08 1.37E-06
vg0421387824 sf0421215877 4 21387824 3.11E-08 1.13E-06
vg0136191693 sf0136190650 1 36191693 1.06E-07 4.51E-07
vg0319269647 sf0319268407 3 19269647 1.79E-07 6.51E-07
vg0221768176 sf0221762307 2 21768176 2.12E-07 7.70E-06
vg0311734309 sf0311733027 3 11734309 3.12E-07 1.21E-07
vg0621728622 sf0621727625 6 21728622 2.02E-06 7.18E-07