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 mr1592 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
vg0222742146 sf0222736277 2 22742146 1.80E-34 2.44E-15
vg0705549134 sf0705548135 7 5549134 8.54E-22 NA
vg0626883082 sf0626882085 6 26883082 1.65E-21 NA
vg0501035247 sf0501035231 5 1035247 1.10E-20 NA
vg0908964730 sf0908963729 9 8964730 3.40E-20 NA
vg0400134690 sf0400133690 4 134690 2.97E-16 4.91E-06
vg0222725003 sf0222719134 2 22725003 NA 2.22E-07