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 mr1386 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
vg0412422045 sf0412412759 4 12422045 7.07E-10 1.42E-06
vg0408349183 sf0408344457 4 8349183 3.21E-08 NA
vg0216308622 sf0216302752 2 16308622 3.59E-08 NA
vg0131924071 sf0131923027 1 31924071 5.52E-08 4.26E-06
vg0216525182 sf0216519312 2 16525182 8.82E-07 NA
vg0131972121 sf0131971077 1 31972121 1.94E-06 NA
vg0602322093 sf0602321094 6 2322093 2.84E-06 4.38E-06
vg1219510809 sf1219482279 12 19510809 5.33E-06 2.00E-06
vg0606120698 sf0606119699 6 6120698 NA 3.57E-06