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 mr1838 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
vg0205287313 sf0205287311 2 5287313 2.13E-36 3.12E-11
vg0205295885 sf0205295883 2 5295885 2.73E-36 2.67E-11
vg0140804736 sf0140803693 1 40804736 5.72E-26 NA
vg0132955231 sf0132954187 1 32955231 2.73E-25 NA
vg0819964769 sf0819962056 8 19964769 6.31E-25 NA
vg1200875101 sf1200874101 12 875101 2.20E-24 NA
vg0205293173 sf0205293171 2 5293173 NA 2.10E-06
vg1016633615 sf1016562388 10 16633615 NA 2.42E-06
vg1214618676 sf1214616016 12 14618676 NA 5.26E-06