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 mr1976 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
vg0400009811 sf0400008811 4 9811 5.89E-09 3.24E-06
vg0400216710 sf0400215710 4 216710 6.66E-09 NA
vg0315358592 sf0315357239 3 15358592 8.25E-09 NA
vg0312560454 sf0312559172 3 12560454 9.95E-09 NA
vg1107376701 sf1107372446 11 7376701 1.98E-08 NA
vg1005306011 sf1005322548 10 5306011 3.04E-07 3.40E-06
vg0400167321 sf0400166321 4 167321 4.59E-07 7.72E-07