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 mr1887 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
vg0136277359 sf0136276316 1 36277359 2.11E-10 2.47E-06
vg0136067759 sf0136066716 1 36067759 3.60E-10 4.79E-06
vg0136063153 sf0136062110 1 36063153 9.09E-10 1.72E-06
vg0710360007 sf0710359013 7 10360007 1.93E-09 6.48E-07
vg1223091482 sf1223057942 12 23091482 3.49E-09 NA
vg0622281780 sf0622280783 6 22281780 1.42E-08 8.41E-06
vg0921118832 sf0921118351 9 21118832 1.71E-08 NA
vg0827168299 sf0827165585 8 27168299 1.00E-07 NA
vg0622322008 sf0622321011 6 22322008 1.21E-07 1.59E-06
vg0201143150 sf0201143150 2 1143150 2.00E-07 3.23E-06
vg0412758955 sf0412749665 4 12758955 8.47E-07 1.71E-07
vg0318113258 sf0318112040 3 18113258 1.96E-06 1.38E-06