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 mr1912 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
vg0226817190 sf0226811321 2 26817190 9.21E-08 NA
vg0318243134 sf0318241916 3 18243134 2.19E-06 4.81E-06
vg0416033751 sf0415861784 4 16033751 4.05E-06 9.14E-07
vg1005803813 sf1005820351 10 5803813 9.27E-06 NA
vg1105283911 sf1105279662 11 5283911 NA 2.85E-06
vg0333810870 sf0333803740 3 33810870 NA 9.42E-06