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 mr1212 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
vg0119414733 sf0119413688 1 19414733 6.69E-09 9.13E-06
vg0719050894 sf0719049901 7 19050894 2.32E-08 5.70E-06
vg0222017648 sf0222011779 2 22017648 1.06E-07 1.60E-06
vg0222042960 sf0222037091 2 22042960 2.18E-07 4.96E-07
vg1000968214 sf1000967190 10 968214 2.93E-06 1.53E-06