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 mr1577 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
vg0723903178 sf0723902184 7 23903178 5.57E-07 5.58E-07
vg0601369122 sf0601368123 6 1369122 5.79E-07 5.79E-07
vg0729077790 sf0729076798 7 29077790 1.22E-06 1.23E-06
vg1214995396 sf1214992738 12 14995396 1.58E-06 1.58E-06
vg0723366162 sf0723365169 7 23366162 1.63E-06 1.63E-06
vg0508305126 sf0508305054 5 8305126 1.75E-06 1.75E-06
vg0609264829 sf0609263830 6 9264829 2.70E-06 2.70E-06
vg0416372665 sf0416200703 4 16372665 3.19E-06 3.19E-06
vg1121965345 sf1121499216 11 21965345 3.83E-06 3.83E-06
vg0109548538 sf0109547514 1 9548538 4.39E-06 4.39E-06
vg1017951405 sf1017880177 10 17951405 4.85E-06 4.85E-06