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 mr1541 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
vg0137887066 sf0137886023 1 37887066 1.34E-46 1.82E-09
vg0520594830 sf0520532271 5 20594830 1.23E-41 NA
vg0626861237 sf0626860240 6 26861237 1.94E-41 NA
vg0217658651 sf0217652781 2 17658651 5.75E-41 NA
vg1017935728 sf1017864500 10 17935728 1.48E-40 NA
vg0815304114 sf0815301400 8 15304114 NA 4.88E-07
vg0142855337 sf0142854293 1 42855337 NA 9.20E-07
vg0317962449 sf0317961231 3 17962449 NA 3.85E-06
vg0138316933 sf0138315890 1 38316933 NA 5.68E-06