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 mr1164 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
vg1011870467 sf1011799282 10 11870467 5.82E-10 NA
vg1210313817 sf1210311230 12 10313817 3.90E-09 NA
vg0202629950 sf0202629948 2 2629950 4.42E-09 NA
vg0313641931 sf0313640648 3 13641931 4.96E-09 NA
vg0506629798 sf0506629739 5 6629798 4.98E-09 NA
vg0122145785 sf0122144740 1 22145785 4.97E-08 2.20E-06
vg0917505707 sf0917504706 9 17505707 1.15E-07 3.90E-06
vg0809822175 sf0809821179 8 9822175 1.48E-07 NA
vg1126916922 sf1126445309 11 26916922 8.79E-06 NA