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 mr1060 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
vg1218162333 sf1218133769 12 18162333 5.06E-11 2.89E-09
vg0700406796 sf0700405796 7 406796 3.45E-09 NA
vg1218522379 sf1218493815 12 18522379 7.39E-09 NA
vg0701643425 sf0701642426 7 1643425 9.50E-09 NA
vg1218118983 sf1218090419 12 18118983 9.66E-09 1.32E-06
vg1218866013 sf1218837448 12 18866013 2.39E-08 3.98E-06
vg1117469649 sf1117003504 11 17469649 1.67E-06 NA
vg0315336415 sf0315335062 3 15336415 1.88E-06 NA
vg1218169236 sf1218140672 12 18169236 3.54E-06 2.70E-08
vg1210418788 sf1210416201 12 10418788 NA 1.72E-06
vg0103143509 sf0103142509 1 3143509 NA 7.64E-06