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 mr1321 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
vg0421984037 sf0421812088 4 21984037 1.39E-10 4.22E-06
vg0700407472 sf0700406472 7 407472 2.04E-10 9.43E-06
vg0703631746 sf0703630747 7 3631746 5.59E-10 NA
vg0529106995 sf0529044350 5 29106995 7.83E-10 4.32E-06
vg0312535741 sf0312534459 3 12535741 8.67E-10 NA
vg1218022381 sf1217993817 12 18022381 2.77E-09 1.22E-07
vg0716064209 sf0716063216 7 16064209 8.66E-09 2.68E-07
vg0320463339 sf0320461850 3 20463339 2.28E-07 NA
vg0205436718 sf0205436718 2 5436718 9.03E-07 NA
vg1218074718 sf1218046154 12 18074718 NA 6.10E-07
vg0216380020 sf0216374150 2 16380020 NA 8.09E-07