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 mr1804 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
vg0820865298 sf0820862585 8 20865298 2.45E-07 2.45E-07
vg0709984451 sf0709983457 7 9984451 3.16E-07 3.16E-07
vg1104978881 sf1104974692 11 4978881 6.91E-07 6.91E-07
vg1214822308 sf1214819649 12 14822308 1.07E-06 1.07E-06
vg1109631523 sf1109626100 11 9631523 1.15E-06 1.15E-06
vg1210390475 sf1210387888 12 10390475 1.42E-06 1.42E-06
vg1007900043 sf1007915653 10 7900043 1.68E-06 1.68E-06
vg0431614108 sf0431429003 4 31614108 2.85E-06 2.85E-06
vg0229918162 sf0229912293 2 29918162 3.86E-06 3.86E-06