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 mr1301 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
vg0417238354 sf0417066395 4 17238354 9.31E-30 5.07E-11
vg0519939017 sf0519876493 5 19939017 4.01E-25 6.44E-10
vg0406910836 sf0406906103 4 6910836 2.12E-21 9.68E-06
vg0410681849 sf0410672551 4 10681849 4.63E-21 3.42E-08
vg0406753488 sf0406748934 4 6753488 4.68E-21 2.89E-08
vg0309190281 sf0309189217 3 9190281 1.07E-20 2.57E-06
vg0211588654 sf0211588650 2 11588654 3.06E-20 1.24E-07
vg0903433897 sf0903432897 9 3433897 3.71E-20 2.79E-07
vg0401725881 sf0401721430 4 1725881 8.23E-20 3.93E-07
vg0111490485 sf0111489461 1 11490485 1.22E-19 9.47E-08
vg0200785919 sf0200785919 2 785919 3.48E-19 4.09E-07
vg0614481201 sf0614480202 6 14481201 1.61E-15 5.45E-07
vg0520474987 sf0520412458 5 20474987 1.73E-14 NA
vg0514347110 sf0514289653 5 14347110 7.21E-14 3.15E-07
vg0509755928 sf0509755857 5 9755928 7.21E-14 3.15E-07
vg0412125651 sf0412116362 4 12125651 NA 7.37E-09
vg0228532699 sf0228526830 2 28532699 NA 1.69E-08
vg0417064731 sf0416892773 4 17064731 NA 2.46E-08
vg0118424879 sf0118423833 1 18424879 NA 1.09E-07
vg0519469410 sf0519406894 5 19469410 NA 1.13E-07
vg1220761649 sf1220728197 12 20761649 NA 1.62E-07
vg0727263961 sf0727262967 7 27263961 NA 3.10E-07
vg0501895878 sf0501895860 5 1895878 NA 4.61E-07
vg0101880727 sf0101879727 1 1880727 NA 5.50E-07
vg0520636147 sf0520573588 5 20636147 NA 5.64E-07
vg0620065391 sf0620064394 6 20065391 NA 6.80E-07