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 mr1161 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
vg0602276709 sf0602275710 6 2276709 5.36E-09 1.04E-06
vg0431601936 sf0431416831 4 31601936 6.18E-09 NA
vg1226987977 sf1226954376 12 26987977 6.63E-09 8.84E-06
vg0722226606 sf0722225613 7 22226606 6.72E-09 NA
vg1215662789 sf1215660086 12 15662789 6.99E-09 NA
vg0721323336 sf0721322343 7 21323336 1.23E-08 NA
vg0400652453 sf0400651452 4 652453 3.78E-08 NA