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 mr1950 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
vg1008554925 sf1008483787 10 8554925 2.87E-07 2.87E-07
vg0907716592 sf0907715592 9 7716592 4.06E-07 4.06E-07
vg0623902712 sf0623901715 6 23902712 1.07E-06 1.07E-06
vg0803244148 sf0803243151 8 3244148 1.30E-06 1.30E-06
vg1211970312 sf1211967647 12 11970312 1.36E-06 1.36E-06
vg0709922564 sf0709921570 7 9922564 1.57E-06 1.57E-06
vg1110034297 sf1110028874 11 10034297 2.36E-06 2.36E-06
vg0527023208 sf0526960564 5 27023208 2.62E-06 2.62E-06
vg0820717502 sf0820714789 8 20717502 3.13E-06 3.13E-06
vg0710830838 sf0710829844 7 10830838 4.24E-06 4.24E-06
vg1006851906 sf1006867529 10 6851906 4.24E-06 4.25E-06