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 mr1078 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
vg0610608095 sf0610607096 6 10608095 6.83E-100 5.37E-34
vg0715669964 sf0715668971 7 15669964 1.43E-56 NA
vg0233932146 sf0233926277 2 33932146 1.63E-56 NA
vg0706880462 sf0706879467 7 6880462 2.54E-56 NA
vg0310442570 sf0310441486 3 10442570 3.75E-56 NA
vg0617624976 sf0617623979 6 17624976 9.01E-50 4.13E-07
vg0610539571 sf0610538572 6 10539571 NA 6.22E-14
vg0610020430 sf0610019431 6 10020430 NA 1.59E-09
vg0614107939 sf0614106940 6 14107939 NA 2.66E-08
vg0610446203 sf0610445204 6 10446203 NA 5.88E-08
vg0610587682 sf0610586683 6 10587682 NA 1.03E-07
vg0609930953 sf0609929954 6 9930953 NA 2.25E-07
vg0610118930 sf0610117931 6 10118930 NA 2.49E-07
vg0610723836 sf0610722837 6 10723836 NA 2.84E-07
vg0208731146 sf0208731145 2 8731146 NA 3.33E-07
vg0610444069 sf0610443070 6 10444069 NA 3.50E-07
vg1115480616 sf1115016929 11 15480616 NA 1.17E-06
vg0920307704 sf0920307223 9 20307704 NA 1.79E-06
vg0617642038 sf0617641041 6 17642038 NA 2.06E-06
vg0417039665 sf0416867707 4 17039665 NA 2.45E-06
vg0612044015 sf0612043016 6 12044015 NA 2.95E-06
vg0610685711 sf0610684712 6 10685711 NA 2.99E-06
vg0610468695 sf0610467696 6 10468695 NA 3.23E-06
vg0615774699 sf0615773701 6 15774699 NA 3.34E-06
vg0616119655 sf0616118657 6 16119655 NA 4.70E-06
vg0612880471 sf0612879472 6 12880471 NA 8.79E-06