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 mr1812 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
vg0301440928 sf0301439926 3 1440928 3.97E-08 9.35E-06
vg0624653755 sf0624652758 6 24653755 4.97E-08 2.88E-06
vg1122688131 sf1122222002 11 22688131 3.74E-07 NA
vg1127591747 sf1127120134 11 27591747 3.70E-06 4.86E-06
vg0413763191 sf0413753905 4 13763191 4.87E-06 NA
vg0922346708 sf0922346227 9 22346708 NA 3.42E-06