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 mr1600 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
vg0222731388 sf0222725519 2 22731388 2.31E-12 3.36E-12
vg0222736681 sf0222730812 2 22736681 1.07E-11 3.12E-14
vg0331745603 sf0331738480 3 31745603 2.72E-09 NA
vg0714895102 sf0714894109 7 14895102 8.54E-08 NA
vg1207863655 sf1207861061 12 7863655 8.95E-08 2.90E-07
vg0900499731 sf0900498731 9 499731 1.79E-07 3.54E-07
vg0222725003 sf0222719134 2 22725003 NA 1.19E-06
vg1214134650 sf1214131990 12 14134650 NA 1.56E-06
vg0922305528 sf0922305047 9 22305528 NA 3.31E-06
vg0516162890 sf0516105374 5 16162890 NA 4.45E-06