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 mr1717 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
vg0220076012 sf0220070144 2 20076012 6.62E-09 6.62E-09
vg1119381446 sf1118915134 11 19381446 3.27E-08 3.27E-08
vg0519136766 sf0519074250 5 19136766 6.23E-07 6.23E-07
vg0221002215 sf0220996347 2 21002215 8.55E-07 8.55E-07
vg0212112209 sf0212112205 2 12112209 1.50E-06 1.50E-06
vg1108343418 sf1108338028 11 8343418 2.03E-06 2.03E-06
vg1101380599 sf1101379600 11 1380599 2.13E-06 2.13E-06
vg0413702577 sf0413693291 4 13702577 2.32E-06 2.32E-06
vg0519909748 sf0519847224 5 19909748 2.41E-06 2.41E-06
vg0322412591 sf0322411080 3 22412591 2.79E-06 2.79E-06
vg0329080105 sf0329073157 3 29080105 3.71E-06 3.71E-06
vg0316144275 sf0316142922 3 16144275 4.26E-06 4.26E-06
vg1218228895 sf1218200331 12 18228895 4.56E-06 4.56E-06