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 mr1977 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
vg0920042560 sf0920042079 9 20042560 7.29E-11 7.33E-06
vg0202488699 sf0202488697 2 2488699 7.92E-11 4.73E-06
vg0715892828 sf0715891835 7 15892828 8.04E-11 8.75E-06
vg0308202313 sf0308201251 3 8202313 9.41E-11 NA
vg0825425930 sf0825423216 8 25425930 1.33E-10 NA
vg0400009004 sf0400008004 4 9004 6.66E-10 4.59E-06
vg0700240229 sf0700239229 7 240229 1.53E-09 2.56E-06
vg0223787451 sf0223781582 2 23787451 4.67E-09 NA
vg0301192756 sf0301191754 3 1192756 8.40E-07 2.70E-06
vg0712108763 sf0712107769 7 12108763 NA 7.87E-07
vg0704131532 sf0704130533 7 4131532 NA 2.01E-06
vg0910453386 sf0910452385 9 10453386 NA 2.59E-06
vg0716068649 sf0716067656 7 16068649 NA 4.24E-06
vg1106571584 sf1106567337 11 6571584 NA 4.89E-06