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 mr1524 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
vg0420711795 sf0420539838 4 20711795 3.88E-08 3.88E-08
vg0424181194 sf0423996055 4 24181194 9.65E-08 9.65E-08
vg0420718113 sf0420546156 4 20718113 1.04E-07 1.04E-07
vg1124705653 sf1124239493 11 24705653 1.79E-07 1.79E-07
vg0516508609 sf0516451091 5 16508609 1.97E-07 1.97E-07
vg0421020772 sf0420848825 4 21020772 4.07E-07 4.07E-07
vg0421384856 sf0421212909 4 21384856 9.67E-07 9.66E-07
vg0110779745 sf0110778721 1 10779745 1.21E-06 1.21E-06
vg0223522667 sf0223516798 2 23522667 1.34E-06 1.34E-06
vg1225484489 sf1225450884 12 25484489 1.68E-06 1.68E-06
vg1215307750 sf1215305048 12 15307750 2.17E-06 2.17E-06
vg0607659813 sf0607658814 6 7659813 2.38E-06 2.38E-06
vg0223522704 sf0223516835 2 23522704 2.48E-06 2.48E-06
vg0921004343 sf0921003862 9 21004343 3.11E-06 3.11E-06
vg0704864945 sf0704863946 7 4864945 3.56E-06 3.56E-06
vg0817557507 sf0817554793 8 17557507 3.62E-06 3.62E-06
vg0817104715 sf0817102001 8 17104715 4.25E-06 4.25E-06
vg0420798136 sf0420626179 4 20798136 4.78E-06 4.78E-06