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 mr1348 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
vg0816861360 sf0816858646 8 16861360 5.26E-07 5.26E-07
vg0827006888 sf0827004174 8 27006888 1.23E-06 1.23E-06
vg0622757649 sf0622756652 6 22757649 3.12E-06 3.12E-06
vg0526045307 sf0525982727 5 26045307 3.46E-06 3.46E-06
vg0624653619 sf0624652622 6 24653619 3.63E-06 3.63E-06
vg1121284164 sf1120818042 11 21284164 4.20E-06 4.20E-06
vg0908364756 sf0908363756 9 8364756 4.47E-06 4.47E-06