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 mr1456 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
vg0618222588 sf0618221591 6 18222588 2.70E-09 4.55E-06
vg0619684836 sf0619683839 6 19684836 9.57E-09 2.60E-06
vg0316586640 sf0316585285 3 16586640 2.70E-08 NA
vg0602338469 sf0602337470 6 2338469 5.11E-08 6.39E-06
vg1224023998 sf1223990451 12 24023998 8.85E-08 NA
vg1209696070 sf1209693479 12 9696070 6.24E-07 NA