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 mr1608 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
vg0217852863 sf0217846994 2 17852863 4.45E-11 1.31E-07
vg0406961183 sf0406956451 4 6961183 1.54E-10 NA
vg0101139584 sf0101138584 1 1139584 1.07E-08 NA
vg0404445369 sf0404440973 4 4445369 1.29E-08 NA
vg0424179235 sf0423994096 4 24179235 2.65E-08 NA
vg0433086358 sf0432901247 4 33086358 1.25E-07 NA
vg0706815440 sf0706814445 7 6815440 1.50E-06 4.71E-06
vg0711639300 sf0711638306 7 11639300 2.85E-06 1.69E-06
vg1019408343 sf1019336898 10 19408343 NA 9.91E-07