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 mr1578 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
vg0232755756 sf0232749887 2 32755756 6.51E-21 2.36E-09
vg0608137746 sf0608136747 6 8137746 3.46E-19 NA
vg0822115787 sf0822113074 8 22115787 4.10E-19 NA
vg1020772860 sf1020701339 10 20772860 4.49E-19 NA
vg1206688034 sf1206686924 12 6688034 4.59E-19 NA
vg0501804785 sf0501804768 5 1804785 9.37E-18 1.49E-06
vg0314122304 sf0314120993 3 14122304 9.73E-17 NA
vg0817844906 sf0817842193 8 17844906 2.44E-15 4.70E-06
vg1218900179 sf1218871614 12 18900179 NA 6.13E-07
vg0501779956 sf0501779939 5 1779956 NA 1.77E-06