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 mr1568 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
vg0423536187 sf0423351044 4 23536187 1.64E-09 1.01E-06
vg0420830827 sf0420658870 4 20830827 4.88E-09 8.85E-07
vg0420830764 sf0420658807 4 20830764 4.99E-09 8.71E-07
vg0916888277 sf0916887276 9 16888277 2.89E-08 NA
vg0402284576 sf0402280171 4 2284576 4.44E-08 NA
vg0921059996 sf0921059515 9 21059996 4.80E-08 3.57E-06
vg1004374773 sf1004391311 10 4374773 2.03E-06 8.66E-08
vg0334515770 sf0334508640 3 34515770 NA 4.86E-07