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 mr1568 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
vg0433516710 sf0433331595 4 33516710 7.96E-08 7.96E-08
vg0717183599 sf0717182606 7 17183599 1.80E-07 1.80E-07
vg0419536798 sf0419364836 4 19536798 4.93E-07 4.93E-07
vg0520413973 sf0520351445 5 20413973 6.45E-07 6.45E-07
vg0423675516 sf0423490373 4 23675516 7.34E-07 7.34E-07
vg0907278736 sf0907277736 9 7278736 7.34E-07 7.34E-07
vg0135062105 sf0135061062 1 35062105 1.01E-06 1.01E-06
vg0907776072 sf0907775072 9 7776072 2.26E-06 2.26E-06
vg1000909798 sf1000908774 10 909798 2.81E-06 2.81E-06
vg0528175919 sf0528113274 5 28175919 3.45E-06 3.45E-06