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 mr1931 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
vg0427368348 sf0427183212 4 27368348 1.63E-10 6.06E-06
vg0142428882 sf0142427838 1 42428882 1.84E-10 NA
vg0324692311 sf0324690390 3 24692311 4.52E-10 NA
vg0617656510 sf0617655513 6 17656510 4.13E-09 7.00E-06
vg0423876581 sf0423691439 4 23876581 7.70E-09 NA
vg0719613006 sf0719612013 7 19613006 1.63E-07 NA
vg0431613586 sf0431428481 4 31613586 1.21E-06 8.42E-08
vg0314448926 sf0314447614 3 14448926 NA 2.62E-06
vg0916242817 sf0916241816 9 16242817 NA 4.44E-06
vg0329897160 sf0329890199 3 29897160 NA 4.71E-06