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 mr1319 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
vg0220034325 sf0220028457 2 20034325 2.03E-09 NA
vg0208268939 sf0208268938 2 8268939 4.29E-09 7.91E-06
vg1203577727 sf1203576726 12 3577727 1.49E-08 NA
vg0410727982 sf0410718684 4 10727982 2.61E-08 NA
vg0132291194 sf0132290150 1 32291194 2.94E-08 NA
vg1122327568 sf1121861439 11 22327568 3.10E-07 4.31E-06
vg1019343613 sf1019272168 10 19343613 5.66E-07 NA
vg0104000380 sf0103999380 1 4000380 3.12E-06 4.95E-06
vg0131938048 sf0131937004 1 31938048 9.93E-06 NA
vg1213499508 sf1213496846 12 13499508 NA 3.56E-06
vg0621629913 sf0621628916 6 21629913 NA 3.64E-06
vg1213653651 sf1213650989 12 13653651 NA 6.29E-06