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 mr1053 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
vg1006197978 sf1006213627 10 6197978 1.45E-09 3.92E-08
vg1009151297 sf1009080118 10 9151297 3.99E-09 9.44E-08
vg1009450104 sf1009378925 10 9450104 6.48E-09 8.47E-09
vg0714251445 sf0714250452 7 14251445 8.38E-09 1.53E-07
vg1121617620 sf1121151497 11 21617620 8.52E-09 1.70E-08
vg1009318290 sf1009247111 10 9318290 1.18E-08 9.09E-09
vg0412457585 sf0412448300 4 12457585 9.23E-08 8.03E-08
vg0813433103 sf0813430656 8 13433103 1.12E-07 1.67E-06
vg0526442423 sf0526379786 5 26442423 4.26E-07 4.60E-06
vg0714252091 sf0714251098 7 14252091 8.70E-07 2.10E-07
vg0905695815 sf0905694815 9 5695815 3.13E-06 3.44E-06
vg0207267578 sf0207267578 2 7267578 4.39E-06 4.72E-06
vg1112909075 sf1112445396 11 12909075 5.42E-06 4.75E-06
vg0407629042 sf0407624309 4 7629042 NA 2.46E-06