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 mr1276 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
vg1213796013 sf1213793351 12 13796013 6.00E-07 6.00E-07
vg0916243027 sf0916242026 9 16243027 7.28E-07 7.28E-07
vg0407000775 sf0406996046 4 7000775 1.00E-06 1.00E-06
vg0916241458 sf0916240457 9 16241458 1.24E-06 1.24E-06
vg1127363594 sf1126891981 11 27363594 2.50E-06 2.50E-06
vg0916790975 sf0916789974 9 16790975 3.50E-06 3.50E-06
vg0716821119 sf0716820126 7 16821119 3.57E-06 3.57E-06
vg0819107411 sf0819104698 8 19107411 3.87E-06 3.87E-06
vg1104258287 sf1104254189 11 4258287 3.95E-06 3.95E-06
vg1014251223 sf1014179989 10 14251223 4.90E-06 4.90E-06
vg0406883410 sf0406878669 4 6883410 6.52E-06 6.52E-06