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 mr1987 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
vg0317581872 sf0317580654 3 17581872 1.70E-10 1.71E-10
vg0320831653 sf0320830163 3 20831653 2.17E-10 2.17E-10
vg0318126392 sf0318125174 3 18126392 6.55E-08 6.56E-08
vg1214622453 sf1214619793 12 14622453 1.26E-07 1.26E-07
vg0320175080 sf0320173591 3 20175080 1.88E-07 1.88E-07
vg0324095631 sf0324093710 3 24095631 3.29E-07 3.29E-07
vg0320161270 sf0320159781 3 20161270 6.35E-07 6.35E-07
vg0320046714 sf0320045225 3 20046714 6.79E-07 6.79E-07
vg0324100933 sf0324099012 3 24100933 7.32E-07 7.32E-07
vg1216141259 sf1216138555 12 16141259 7.92E-07 7.92E-07
vg0319498343 sf0319496854 3 19498343 9.23E-07 9.24E-07
vg0322035566 sf0322034073 3 22035566 9.31E-07 9.31E-07
vg0318542792 sf0318541574 3 18542792 1.40E-06 1.40E-06
vg0321537632 sf0321536142 3 21537632 1.43E-06 1.43E-06
vg1216124169 sf1216121465 12 16124169 1.61E-06 1.61E-06
vg0320151239 sf0320149750 3 20151239 1.79E-06 1.79E-06
vg0321218638 sf0321217148 3 21218638 1.90E-06 1.90E-06
vg0321044536 sf0321043046 3 21044536 1.97E-06 1.97E-06
vg0324097319 sf0324095398 3 24097319 2.46E-06 2.46E-06
vg0320749463 sf0320747973 3 20749463 2.46E-06 2.46E-06