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 mr1275 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
vg0217652051 sf0217646181 2 17652051 4.50E-07 4.50E-07
vg1112990301 sf1112526622 11 12990301 5.31E-07 5.31E-07
vg0218865603 sf0218859734 2 18865603 6.79E-07 6.79E-07
vg0218856412 sf0218850543 2 18856412 7.19E-07 7.19E-07
vg0131782604 sf0131781560 1 31782604 8.92E-07 8.92E-07
vg0407782064 sf0407777332 4 7782064 1.16E-06 1.16E-06
vg0904281172 sf0904280172 9 4281172 1.39E-06 1.39E-06
vg0235128728 sf0235122859 2 35128728 1.47E-06 1.47E-06
vg0313176403 sf0313175121 3 13176403 1.67E-06 1.67E-06
vg0813601775 sf0813599060 8 13601775 1.70E-06 1.70E-06
vg0913502387 sf0913501386 9 13502387 2.07E-06 2.07E-06
vg1127125428 sf1126653815 11 27125428 2.09E-06 2.09E-06
vg0907586801 sf0907585801 9 7586801 2.23E-06 2.23E-06
vg0809364764 sf0809363768 8 9364764 2.65E-06 2.65E-06
vg0122697025 sf0122695980 1 22697025 2.73E-06 2.73E-06
vg0401502812 sf0401498362 4 1502812 2.89E-06 2.89E-06
vg0421169357 sf0420997409 4 21169357 3.03E-06 3.03E-06
vg0217863794 sf0217857925 2 17863794 3.16E-06 3.16E-06
vg0715352632 sf0715351639 7 15352632 3.44E-06 3.45E-06
vg1208858063 sf1208855471 12 8858063 3.50E-06 3.50E-06
vg0615549887 sf0615548889 6 15549887 4.10E-06 4.10E-06
vg0313073263 sf0313071981 3 13073263 6.96E-06 6.95E-06