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 mr1391 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
vg0318103123 sf0318101905 3 18103123 3.79E-08 6.00E-07
vg1210564472 sf1210561885 12 10564472 7.07E-08 1.64E-06
vg1210406437 sf1210403850 12 10406437 8.04E-08 1.38E-06
vg0318051636 sf0318050418 3 18051636 1.07E-07 2.96E-07
vg0140615189 sf0140614146 1 40615189 1.14E-07 1.38E-06
vg0421026126 sf0420854179 4 21026126 2.37E-07 2.42E-06
vg0414114398 sf0414105113 4 14114398 9.64E-06 3.43E-07