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 mr1901 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
vg0217847717 sf0217841848 2 17847717 2.77E-11 1.17E-06
vg0217105238 sf0217099368 2 17105238 4.37E-11 3.97E-07
vg0214797114 sf0214791244 2 14797114 3.24E-09 5.29E-06
vg0131804162 sf0131803118 1 31804162 6.02E-09 6.27E-06
vg0522701149 sf0522638591 5 22701149 1.06E-08 1.24E-06
vg0210593337 sf0210593335 2 10593337 2.03E-08 5.94E-07
vg0132047743 sf0132046699 1 32047743 1.28E-06 NA
vg0135939616 sf0135938573 1 35939616 NA 5.53E-06