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 mr1606 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
vg1214731491 sf1214728832 12 14731491 9.05E-10 NA
vg0403315819 sf0403311422 4 3315819 4.69E-09 6.48E-07
vg0314727656 sf0314726343 3 14727656 9.19E-09 NA
vg0921500312 sf0921499831 9 21500312 9.40E-09 3.97E-06
vg0203536993 sf0203536991 2 3536993 9.58E-09 NA
vg0614537609 sf0614536610 6 14537609 1.17E-07 4.29E-06