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 mr1614 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
vg0113820276 sf0113819250 1 13820276 7.93E-10 NA
vg1125605977 sf1125139816 11 25605977 9.70E-09 NA
vg1117178010 sf1116711862 11 17178010 1.18E-08 NA
vg1218162333 sf1218133769 12 18162333 1.30E-08 2.89E-06
vg0520118958 sf0520056433 5 20118958 1.41E-08 NA
vg1218074718 sf1218046154 12 18074718 6.18E-07 3.44E-06
vg0202698817 sf0202698815 2 2698817 1.13E-06 3.40E-06
vg1106508580 sf1106504332 11 6508580 1.72E-06 NA
vg1218169215 sf1218140651 12 18169215 NA 2.42E-07
vg0103143509 sf0103142509 1 3143509 NA 1.51E-06