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 mr1702 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
vg0303447913 sf0303446909 3 3447913 1.60E-10 NA
vg0820968537 sf0820965824 8 20968537 1.63E-10 NA
vg1121817225 sf1121351102 11 21817225 2.87E-10 NA
vg0800207863 sf0800206863 8 207863 7.52E-10 NA
vg0607999806 sf0607998807 6 7999806 1.83E-09 NA
vg0417918664 sf0417746705 4 17918664 3.05E-07 NA
vg0119495785 sf0119494740 1 19495785 1.17E-06 4.77E-06
vg1214656787 sf1214654127 12 14656787 4.16E-06 9.89E-07
vg0721376419 sf0721375426 7 21376419 9.90E-06 NA
vg0909297791 sf0909296790 9 9297791 NA 1.13E-06
vg1207853018 sf1207850424 12 7853018 NA 1.94E-06
vg0433410262 sf0433225151 4 33410262 NA 3.12E-06
vg0918843192 sf0918842192 9 18843192 NA 3.21E-06
vg1106630123 sf1106625876 11 6630123 NA 4.88E-06
vg0433421279 sf0433236168 4 33421279 NA 5.29E-06
vg1215626576 sf1215623873 12 15626576 NA 5.39E-06