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 mr1500 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
vg0130802275 sf0130801231 1 30802275 1.53E-07 1.52E-07
vg1219572926 sf1219544396 12 19572926 2.51E-07 2.51E-07
vg1115823556 sf1115359864 11 15823556 9.92E-07 9.90E-07
vg0300265158 sf0300264158 3 265158 1.94E-06 1.94E-06
vg0224128536 sf0224122667 2 24128536 2.63E-06 2.62E-06
vg1215178307 sf1215175643 12 15178307 2.90E-06 2.90E-06
vg1118881298 sf1118415107 11 18881298 3.27E-06 3.26E-06
vg0321148371 sf0321146881 3 21148371 4.52E-06 4.52E-06
vg1115880748 sf1115415618 11 15880748 4.91E-06 4.91E-06