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 mr1660 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
vg1218110790 sf1218082226 12 18110790 1.59E-10 3.31E-06
vg1218168835 sf1218140271 12 18168835 7.53E-09 2.78E-06
vg1217606407 sf1217600362 12 17606407 6.39E-08 NA
vg1222488812 sf1222455251 12 22488812 8.12E-08 7.89E-06
vg0304596104 sf0304595106 3 4596104 8.51E-08 NA
vg0520503098 sf0520440569 5 20503098 6.10E-07 NA
vg1207276357 sf1207273764 12 7276357 1.11E-06 2.09E-06
vg0406849851 sf0406845296 4 6849851 1.57E-06 4.60E-06
vg0521701169 sf0521638611 5 21701169 4.15E-06 5.24E-06