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 mr1825 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
vg1005865739 sf1005882277 10 5865739 2.90E-12 1.02E-06
vg1005804033 sf1005820571 10 5804033 1.59E-11 3.90E-07
vg0403275975 sf0403271578 4 3275975 1.27E-10 4.94E-06
vg0715860267 sf0715859274 7 15860267 2.64E-09 NA
vg0820461846 sf0820459133 8 20461846 4.42E-09 NA
vg1209554698 sf1209552107 12 9554698 7.16E-09 NA
vg1217578034 sf1217571989 12 17578034 2.36E-08 NA
vg1006601763 sf1006617386 10 6601763 3.76E-08 2.36E-06
vg1008541700 sf1008470562 10 8541700 2.81E-07 2.09E-07
vg1210098198 sf1210095609 12 10098198 3.40E-06 4.60E-06
vg0813652482 sf0813649767 8 13652482 3.77E-06 4.61E-06
vg0130267498 sf0130266453 1 30267498 NA 3.49E-06