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 mr1159 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
vg0516027523 sf0515970031 5 16027523 3.20E-08 3.20E-08
vg0623833223 sf0623832226 6 23833223 5.19E-08 5.19E-08
vg0217797694 sf0217791825 2 17797694 5.20E-08 5.20E-08
vg1109263217 sf1109257794 11 9263217 2.34E-07 2.34E-07
vg0922316114 sf0922315633 9 22316114 3.97E-07 3.97E-07
vg1119034181 sf1118567869 11 19034181 1.04E-06 1.04E-06
vg0407996034 sf0407991303 4 7996034 1.12E-06 1.12E-06
vg1119464392 sf1118998080 11 19464392 2.36E-06 2.36E-06
vg0518855326 sf0518792810 5 18855326 2.49E-06 2.49E-06