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 mr1237 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
vg0610567538 sf0610566539 6 10567538 6.29E-62 7.77E-18
vg0719259692 sf0719258699 7 19259692 5.62E-44 1.63E-06
vg0719149750 sf0719148757 7 19149750 1.68E-43 1.37E-06
vg0617319066 sf0617318069 6 17319066 3.04E-38 1.88E-06
vg0402467794 sf0402463392 4 2467794 1.62E-37 NA
vg0304969634 sf0304968636 3 4969634 6.02E-37 NA
vg1201521385 sf1201520385 12 1521385 8.34E-35 NA
vg0610788671 sf0610787672 6 10788671 NA 2.27E-09
vg0610676484 sf0610675485 6 10676484 NA 8.39E-08
vg0610567093 sf0610566094 6 10567093 NA 3.53E-07
vg0611127099 sf0611126100 6 11127099 NA 4.16E-07
vg0617631923 sf0617630926 6 17631923 NA 5.47E-07
vg0610273485 sf0610272486 6 10273485 NA 5.62E-07
vg1220182193 sf1220153635 12 20182193 NA 2.47E-06
vg0916036140 sf0916035139 9 16036140 NA 3.02E-06
vg0719007754 sf0719006761 7 19007754 NA 3.47E-06
vg1116692722 sf1116227599 11 16692722 NA 3.48E-06