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 mr1906 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
vg0225148780 sf0225142911 2 25148780 3.95E-10 NA
vg0434711477 sf0434526367 4 34711477 1.29E-09 1.11E-06
vg0817589164 sf0817586451 8 17589164 5.72E-09 NA
vg0909486564 sf0909485563 9 9486564 9.88E-09 NA
vg0603928595 sf0603927596 6 3928595 1.60E-08 NA
vg1005292809 sf1005309346 10 5292809 1.01E-06 4.06E-06
vg1207088649 sf1207087539 12 7088649 7.11E-06 1.27E-07
vg1214616847 sf1214614187 12 14616847 NA 2.66E-06
vg1215566706 sf1215564003 12 15566706 NA 2.75E-06
vg0216740793 sf0216734923 2 16740793 NA 3.12E-06
vg0124832071 sf0124831027 1 24832071 NA 4.68E-06