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 mr1531 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
vg0821091267 sf0821088554 8 21091267 3.16E-09 2.92E-07
vg1124716076 sf1124249916 11 24716076 1.28E-08 NA
vg0140621718 sf0140620675 1 40621718 1.34E-08 NA
vg1218622121 sf1218593557 12 18622121 3.10E-08 4.63E-06
vg0910849082 sf0910848081 9 10849082 7.01E-08 NA
vg0804772741 sf0804771744 8 4772741 8.79E-08 2.77E-06
vg1211686189 sf1211683525 12 11686189 8.58E-07 NA
vg0417801766 sf0417629804 4 17801766 6.49E-06 NA
vg0721439672 sf0721438679 7 21439672 NA 8.58E-06