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 mr1845 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
vg0212556837 sf0212556833 2 12556837 1.66E-24 NA
vg0819249760 sf0819247047 8 19249760 3.41E-24 5.23E-06
vg0819198916 sf0819196203 8 19198916 9.22E-24 1.24E-06
vg0521675477 sf0521612919 5 21675477 2.06E-23 NA
vg0816278155 sf0816275441 8 16278155 2.28E-22 NA
vg0204375661 sf0204375658 2 4375661 2.31E-22 NA
vg1001392877 sf1001391854 10 1392877 NA 1.50E-07
vg0818666272 sf0818663559 8 18666272 NA 2.41E-07
vg1218873031 sf1218844466 12 18873031 NA 3.51E-07
vg1216058251 sf1216055547 12 16058251 NA 7.17E-07
vg1218119528 sf1218090964 12 18119528 NA 4.64E-06
vg1104173599 sf1104169501 11 4173599 NA 8.44E-06