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 mr1063 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
vg0722226606 sf0722225613 7 22226606 2.34E-10 NA
vg1200675049 sf1200674049 12 675049 3.52E-09 NA
vg0528836237 sf0528773592 5 28836237 3.63E-09 NA
vg1214703763 sf1214701104 12 14703763 4.45E-09 NA
vg0913947365 sf0913946364 9 13947365 6.94E-09 3.56E-06
vg0402160287 sf0402155882 4 2160287 2.57E-08 7.58E-07
vg0317273290 sf0317272100 3 17273290 2.83E-08 3.86E-06
vg0820830545 sf0820827832 8 20830545 6.12E-06 NA