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 mr1271 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
vg0908594707 sf0908593706 9 8594707 3.96E-10 NA
vg1126876356 sf1126404743 11 26876356 2.39E-09 NA
vg1016195645 sf1016124417 10 16195645 2.12E-08 NA
vg0622341253 sf0622340256 6 22341253 2.87E-08 NA
vg1217956699 sf1217928135 12 17956699 2.96E-08 NA
vg1015019314 sf1014948080 10 15019314 8.21E-07 NA
vg0915042464 sf0915041463 9 15042464 1.72E-06 7.42E-06
vg1117008231 sf1116542083 11 17008231 6.60E-06 1.05E-06