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 mr1742 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
vg1107621144 sf1107616889 11 7621144 1.53E-11 5.58E-07
vg0329268317 sf0329261357 3 29268317 9.61E-11 6.67E-06
vg0520039079 sf0519976555 5 20039079 2.86E-10 NA
vg0303955124 sf0303954120 3 3955124 7.63E-10 NA
vg1116062677 sf1115597549 11 16062677 1.16E-09 NA
vg0520397801 sf0520335273 5 20397801 1.36E-08 4.65E-06
vg0433154468 sf0432969356 4 33154468 5.22E-08 3.92E-06