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 mr1802 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
vg0920894235 sf0920893754 9 20894235 4.75E-07 4.75E-07
vg0425123848 sf0424938709 4 25123848 1.00E-06 1.00E-06
vg0816052546 sf0816049832 8 16052546 1.04E-06 1.04E-06
vg0209141112 sf0209141110 2 9141112 1.62E-06 1.62E-06
vg0706269309 sf0706268310 7 6269309 1.84E-06 1.84E-06
vg0708399861 sf0708398866 7 8399861 2.66E-06 2.67E-06
vg0129618796 sf0129617751 1 29618796 3.35E-06 3.36E-06
vg0334564078 sf0334556948 3 34564078 4.72E-06 4.72E-06
vg1224874446 sf1224840900 12 24874446 4.97E-06 4.98E-06