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 mr1713 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
vg0401056244 sf0401051795 4 1056244 4.58E-08 8.64E-06
vg0400149978 sf0400148978 4 149978 4.12E-07 1.93E-06
vg1213717963 sf1213715301 12 13717963 4.95E-06 1.28E-06
vg0917117042 sf0917116041 9 17117042 9.50E-06 NA
vg0316516166 sf0316514811 3 16516166 NA 1.02E-06