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 mr1744 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
vg0527296981 sf0527234337 5 27296981 5.77E-08 7.19E-06
vg0915839955 sf0915838954 9 15839955 7.71E-08 8.47E-06
vg0527290052 sf0527227408 5 27290052 7.95E-08 6.59E-06
vg0225036220 sf0225030351 2 25036220 1.26E-06 NA
vg1128801321 sf1128278100 11 28801321 2.90E-06 9.95E-06
vg0417803450 sf0417631488 4 17803450 3.66E-06 1.72E-06
vg0122694201 sf0122693156 1 22694201 5.19E-06 3.45E-06