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 mr1168 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
vg1000080974 sf1000079974 10 80974 7.49E-30 4.87E-07
vg0700174113 sf0700173113 7 174113 1.59E-28 NA
vg0524183671 sf0524121090 5 24183671 6.83E-28 NA
vg0614879830 sf0614878831 6 14879830 1.65E-27 3.66E-06
vg0328116174 sf0328109228 3 28116174 2.84E-27 NA
vg1119446198 sf1118979886 11 19446198 1.16E-22 NA
vg0626459833 sf0626458836 6 26459833 2.73E-22 1.92E-06
vg0626440887 sf0626439890 6 26440887 7.43E-22 2.56E-06
vg0113613619 sf0113612593 1 13613619 NA 1.15E-07
vg1000073755 sf1000072755 10 73755 NA 3.46E-07
vg0311227346 sf0311226064 3 11227346 NA 4.62E-06
vg0900043120 sf0900042120 9 43120 NA 4.72E-06
vg0713275063 sf0713274070 7 13275063 NA 4.97E-06