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 mr1104 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
vg0719208938 sf0719207945 7 19208938 2.43E-26 2.45E-16
vg0719001862 sf0719000869 7 19001862 1.40E-25 2.14E-18
vg0719270235 sf0719269242 7 19270235 2.08E-18 5.32E-09
vg0431282979 sf0431097869 4 31282979 1.06E-16 4.56E-08
vg0431302885 sf0431117779 4 31302885 1.57E-16 2.11E-08
vg0717197101 sf0717196108 7 17197101 3.10E-15 6.03E-10
vg0719007683 sf0719006690 7 19007683 2.00E-14 4.23E-10
vg0717307582 sf0717306589 7 17307582 6.63E-13 7.50E-07
vg0719134835 sf0719133842 7 19134835 2.40E-12 2.75E-07
vg1201545939 sf1201544939 12 1545939 2.07E-11 1.41E-07
vg0613011415 sf0613010416 6 13011415 1.06E-10 3.69E-08
vg0429316121 sf0429130987 4 29316121 2.87E-10 8.51E-07
vg0908143257 sf0908142257 9 8143257 3.80E-10 8.29E-08
vg0615939448 sf0615938450 6 15939448 3.01E-09 8.58E-07
vg0226057933 sf0226052064 2 26057933 4.74E-09 1.69E-07
vg0719465974 sf0719464981 7 19465974 5.54E-09 3.42E-07
vg0706565900 sf0706564905 7 6565900 8.02E-09 1.63E-06
vg0718985437 sf0718984444 7 18985437 1.10E-08 1.22E-08
vg0719186794 sf0719185801 7 19186794 6.40E-08 1.06E-06
vg0504291251 sf0504291228 5 4291251 3.07E-07 8.45E-08
vg1210130843 sf1210128254 12 10130843 8.76E-07 NA
vg0402151540 sf0402147135 4 2151540 3.88E-06 2.13E-06
vg0319785500 sf0319784011 3 19785500 NA 2.09E-06
vg0628573935 sf0628572937 6 28573935 NA 2.11E-06